# HG changeset patch
# User iracooke
# Date 1434512619 14400
# Node ID dfaea053e32fbd395125b60ffb2145c63a2b856f
# Parent  2cafc729b2ae9e1580d281ca29103ceb861c6784
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c

diff -r 2cafc729b2ae -r dfaea053e32f README.rst
--- a/README.rst	Sun May 31 09:05:57 2015 -0400
+++ b/README.rst	Tue Jun 16 23:43:39 2015 -0400
@@ -14,8 +14,8 @@
 Includes tool wrappers for SearchGUI and PeptideShaker. The SearchGUI tool takes any number of mgf files and performs searches on these.  It creates a large zip archive with all search results, the original database and spectra.  This can then be fed to the PeptideShaker tool which merges the results and performs peptide and protein inference.
 
 
-Configuration
--------------
+General Requirements
+--------------------
 
 This tool requires a Java runtime 1.6 or greater to work. To avoid out of memory errors you should set the maximum heapspace for java processes as the default is most likely too small. For example, to set this in your shell:
 
@@ -27,7 +27,20 @@
 
 It is also possible to set this on a per tool basis using advanced features of the galaxy job config system.
 
-Note:
+MSAmanda on linux
+-----------------
+
+Running MS Amanda on Linux requires that you have Mono installed. Mono 3.2.1 or newer is required.  If you install via the toolshed Mono should be installed automatically, however if this does not work you can install it manually.
+  
+On ubuntu Mono can be installed as follows
+
+	sudo apt-get install mono-runtime
+	sudo apt-get install libmono-system-core4.0-cil
+
+For more help on installing Mono please see http://www.mono-project.com/download. 
+
+Note
+----
 
 - PeptideShaker may require xvfb to simulate an X environment if this is installed on a headless server.
 
@@ -75,4 +88,6 @@
 * Cody Wang
 * Fred Sadler
 * John Chilton <jmchilton@gmail.com>
+* Gerben Menschaert
+* Elvis Ndah
 * Minnesota Supercomputing Institute, Univeristy of Minnesota
diff -r 2cafc729b2ae -r dfaea053e32f peptide_shaker.xml
--- a/peptide_shaker.xml	Sun May 31 09:05:57 2015 -0400
+++ b/peptide_shaker.xml	Tue Jun 16 23:43:39 2015 -0400
@@ -1,13 +1,13 @@
-<tool id="peptide_shaker" name="Peptide Shaker" version="0.38.0">
+<tool id="peptide_shaker" name="Peptide Shaker" version="0.40.0">
     <description>
         Perform protein identification using various search engines based on results from SearchGUI
     </description>
-    <requirements>
-        <requirement type="package" version="0.38">peptide_shaker</requirement>
-    </requirements>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <requirements>
+        <requirement type="package" version="0.40">peptide_shaker</requirement>
+    </requirements>
     <expand macro="stdio" />
     <command>
 <![CDATA[
@@ -161,7 +161,7 @@
 ]]>
     </command>
     <inputs>
-        <param name="searchgui_input" format="searchgui_zip" type="data" label="Compressed SearchGUI results"
+        <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
             help="SearchGUI Results from History"/>
 
         <conditional name="species_type">
@@ -545,7 +545,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
             <param name="species_type_selector" value="no_species_type"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="no"/>
@@ -555,13 +555,13 @@
             <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
         </test>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
             <param name="species_type_selector" value="no_species_type"/>
             <param name="processing_options_selector" value="no"/>
             <param name="filtering_options_selector" value="yes"/>
             <param name="min_peptide_length" value="1"/>
             <param name="outputs" value="0,1,2,3,4,5,6,7"/>
-            <output name="output_certificate" file="peptide_shaker_certificate_result2.tabular" ftype="tabular" lines_diff="4"/>
+            <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/>
             <output name="output_hierarchical" file="peptide_shaker_hierarchical_result2.tabular" ftype="tabular" />
             <output name="output_psm" file="peptide_shaker_psm_result2.tabular" ftype="tabular" />
             <output name="output_psm_phosphorylation" file="peptide_shaker_psm_phoshorylation_result2.tabular" ftype="tabular" />
@@ -571,7 +571,7 @@
             <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
         </test>
         <test>
-            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_zip"/>
+            <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
             <param name="species_type_selector" value="Vertebrates"/>
             <param name="species" value="Human (Homo sapiens)"/>
             <param name="processing_options_selector" value="no"/>
diff -r 2cafc729b2ae -r dfaea053e32f repository_dependencies.xml
--- a/repository_dependencies.xml	Sun May 31 09:05:57 2015 -0400
+++ b/repository_dependencies.xml	Tue Jun 16 23:43:39 2015 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="Required proteomics dependencies.">
-    <repository changeset_revision="d1ea609e57d4" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="300fc3aa6954" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 2cafc729b2ae -r dfaea053e32f searchgui.xml
--- a/searchgui.xml	Sun May 31 09:05:57 2015 -0400
+++ b/searchgui.xml	Tue Jun 16 23:43:39 2015 -0400
@@ -1,13 +1,14 @@
-<tool id="search_gui" name="Search GUI" version="1.27.0">
+<tool id="search_gui" name="Search GUI" version="1.28.0">
     <description>
         Perform protein identification using various search engines and prepare results for input to Peptide Shaker
     </description>
-    <requirements>
-        <requirement type="package" version="1.27">searchgui</requirement>
-    </requirements>
     <macros>
         <import>macros.xml</import>
     </macros>
+    <requirements>
+        <requirement type="package" version="1.28">searchgui</requirement>
+        <environment_variable name="LC_ALL" action="set_to">C</environment_variable>        
+    </requirements>
     <expand macro="stdio" />
     <command>
 <![CDATA[
@@ -34,7 +35,7 @@
             java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
             rm input_database.fasta &&
             cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
-            ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
+            ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
         #end if
 
         #####################################################
@@ -48,43 +49,196 @@
 
             -db input_database.fasta
 
-            #if $advanced.advanced_type_selector == "advanced":
+            #if $xtandem.xtandem_advanced == "yes"
+
+                -xtandem_npeaks ${xtandem.xtandem_npeaks}
+                -xtandem_min_peaks ${xtandem.xtandem_min_peaks}
+                -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz}
+                -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass}
+                -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr}
+                -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range}
+                -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl} 
+                -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro} 
+                -xtandem_stp_bias ${xtandem.xtandem_stp_bias} 
+                -xtandem_evalue ${xtandem.xtandem_evalue} 
+                -xtandem_output_proteins ${xtandem.xtandem_output_proteins} 
+                -xtandem_output_sequences ${xtandem.xtandem_output_sequences} 
+                -xtandem_output_spectra ${xtandem.xtandem_output_spectra}
+                ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path}
+
+                #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"
+                    -xtandem_refine 1
+                    -xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc}
+                    -xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi}
+                    -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut}
+                    -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps}
+                    -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt}
+                    -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot}
+                    -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
+                    
+                #end if
+            #end if
 
-                #if $advanced.xtandem.xtandem_selector == "yes"
+            #if $omssa.omssa_advanced == "yes"
+                -omssa_hitlist_length ${omssa.hitlist_length}
+                -omssa_remove_prec ${omssa.remove_precursor}
+                -omssa_scale_prec ${omssa.scale_precursor}
+                -omssa_estimate_charge ${omssa.estimate_charge}
+
+                -omssa_memory ${omssa.omssa_memory}
+                -omssa_isotopes ${omssa.omssa_isotopes} 
+                -omssa_neutron ${omssa.omssa_neutron} 
+                -omssa_low_intensity "${omssa.omssa_low_intensity}" 
+                -omssa_high_intensity ${omssa.omssa_high_intensity} 
+                -omssa_intensity_incr ${omssa.omssa_intensity_incr} 
+                -omssa_single_window_wd ${omssa.omssa_single_window_wd} 
+                -omssa_double_window_wd ${omssa.omssa_double_window_wd} 
+                -omssa_single_window_pk ${omssa.omssa_single_window_pk} 
+                -omssa_double_window_pk ${omssa.omssa_double_window_pk} 
+                -omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks} 
+                -omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks} 
+                -omssa_min_peaks ${omssa.omssa_min_peaks} 
+                -omssa_methionine ${omssa.omssa_methionine} 
+                -omssa_max_ladders ${omssa.omssa_max_ladders} 
+                -omssa_max_frag_charge ${omssa.omssa_max_frag_charge} 
+                -omssa_fraction ${omssa.omssa_fraction} 
+                -omssa_plus_one ${omssa.omssa_plus_one} 
+                -omssa_charge ${omssa.omssa_charge} 
+                -omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum} 
+                -omssa_forward ${omssa.omssa_forward} 
+                -omssa_rewind ${omssa.omssa_rewind} 
+                -omssa_max_frag_series ${omssa.omssa_max_frag_series} 
+                -omssa_corr ${omssa.omssa_corr} 
+                -omssa_consecutive_p ${omssa.omssa_consecutive_p} 
+                -omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue} 
+                -omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue} 
+                -omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue} 
+                -omssa_max_evalue ${omssa.omssa_max_evalue} 
+                -omssa_hitlist_charge ${omssa.omssa_hitlist_charge} 
+                -omssa_min_pep_length ${omssa.omssa_min_pep_length} 
+                -omssa_max_pep_length ${omssa.omssa_max_pep_length} 
+                -omssa_format ${omssa.omssa_format}   
+            #end if
 
-                    -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
-                    -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
-                    -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
-                    -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
-                    -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
+            #if $msgf.msgf_advanced == "yes"
+                -msgf_decoy ${msgf.msgf_decoy}
+                -msgf_min_pep_length ${msgf.msgf_min_pep_length}
+                -msgf_max_pep_length ${msgf.msgf_max_pep_length}
+                -msgf_termini ${msgf.msgf_termini}
+                -msgf_num_ptms ${msgf.msgf_num_ptms}
+                -msgf_instrument ${msgf.msgf_instrument} 
+                -msgf_fragmentation ${msgf.msgf_fragmentation}
+                -msgf_protocol ${msgf.msgf_protocol} 
+                -msgf_num_matches ${msgf.msgf_num_matches} 
+                -msgf_additional ${msgf.msgf_additional} 
+                -msgf_isotope_low ${msgf.msgf_isotope_low} 
+                -msgf_isotope_high ${msgf.msgf_isotope_high} 
+            #end if
+            
+            #if $ms_amanda.ms_amanda_advanced == "yes"
+                 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
+                 -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
+                 -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument} 
+                 -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} 
+                 -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
+            #end if
+            
+            #if $myrimatch.myrimatch_advanced == "yes"
+                -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
+                -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
+                -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
+                -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
+                -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
+                -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
+                -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
+                -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
+                -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
+                -myrimatch_termini ${myrimatch.myrimatch_termini}
+                -myrimatch_plus_three ${myrimatch.myrimatch_plus_three}
+                -myrimatch_xcorr ${myrimatch.myrimatch_xcorr}
+                -myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff}
+                -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes}
+                -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier}
+                -myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
+                -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}                    
+            #end if
 
-                    #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
-                        -xtandem_refine 1
-                        -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
-                        -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
-                        -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
-                        -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
-                        -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
-                    #end if
+            #if $tide.tide_advanced == "yes"
+                -tide_num_ptms ${tide.tide_num_ptms}
+                -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
+                -tide_min_pep_length ${tide.tide_min_pep_length}
+                -tide_max_pep_length ${tide.tide_max_pep_length}
+                -tide_min_prec_mass ${tide.tide_min_prec_mass}
+                -tide_max_prec_mass ${tide.tide_max_prec_mass}
+                -tide_decoy_format ${tide.tide_decoy_format}
+                -tide_keep_terminals ${tide.tide_keep_terminals}
+            
+                -tide_output_folder ${tide.tide_output_folder}
+                -tide_print_peptides ${tide.tide_print_peptides}
+                -tide_verbosity ${tide.tide_verbosity}
+                -tide_monoisotopic ${tide.tide_monoisotopic}
+                -tide_clip_n_term ${tide.tide_clip_n_term}
+                -tide_digestion_type ${tide.tide_digestion_type}
+                -tide_compute_sp ${tide.tide_compute_sp}
+                -tide_max_psms ${tide.tide_max_psms}
+                -tide_compute_p ${tide.tide_compute_p}
+                -tide_min_spectrum_mz ${tide.tide_min_spectrum_mz}
+                -tide_max_spectrum_mz ${tide.tide_max_spectrum_mz}
+                -tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks}
+                -tide_spectrum_charges ${tide.tide_spectrum_charges}
+                -tide_remove_prec ${tide.tide_remove_prec}
+                -tide_remove_prec_tol ${tide.tide_remove_prec_tol}
+                -tide_progress_indicator ${tide.tide_progress_indicator}
+                -tide_use_flanking ${tide.tide_use_flanking}
+                -tide_use_neutral_losses ${tide.tide_use_neutral_losses}
+                -tide_mz_bin_width ${tide.tide_mz_bin_width}
+                -tide_mz_bin_offset ${tide.tide_mz_bin_offset}
+                -tide_concat ${tide.tide_concat}
+                -tide_export_text ${tide.tide_export_text}
+                -tide_export_sqt ${tide.tide_export_sqt}
+                -tide_export_pepxml ${tide.tide_export_pepxml}
+                -tide_export_mzid ${tide.tide_export_mzid}
+                -tide_export_pin ${tide.tide_export_pin}
+                -tide_remove_temp ${tide.tide_remove_temp}
+            #end if
+
+            #if $comet.comet_advanced == "yes"
+
+                #if $comet.comet_spectrum.comet_spectrum_selector == "yes"
+                    -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
+                    -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}
+                    -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec}
+
+
+                     #if $comet.comet_spectrum.comet_remove_prec == "1"
+                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
+                     #end if
+                     
+                     #if $comet.comet_spectrum.comet_remove_prec == "2"
+                        -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
+                     #end if
+                     
+                    -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
+                    -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
                 #end if
 
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa_hitlist_length ${advanced.omssa.hitlist_length}
-                    -omssa_remove_prec ${advanced.omssa.remove_precursor}
-                    -omssa_scale_prec ${advanced.omssa.scale_precursor}
-                    -omssa_estimate_charge ${advanced.omssa.estimate_charge}
+                #if $comet.comet_search.comet_search_selector == "yes"
+                    -comet_enzyme_type ${comet.comet_search.comet_enzyme_type}
+                    -comet_isotope_correction ${comet.comet_search.comet_isotope_correction}
+                    -comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass}
+                    -comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass}
+                    -comet_num_matches ${comet.comet_search.comet_num_matches}
+                    -comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge}
+                    -comet_remove_meth ${comet.comet_search.comet_remove_meth}
+                    -comet_batch_size ${comet.comet_search.comet_batch_size}
+                    -comet_num_ptms ${comet.comet_search.comet_num_ptms}
                 #end if
 
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
-                    -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
-                    -msgf_termini ${advanced.msgf.msgf_termini}
-                    -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
+                #if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
+                    -comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset}
+                    -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
+                    -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
                 #end if
-
-                ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                ##end if
-
             #end if
 
         2> $temp_stderr)
@@ -100,10 +254,13 @@
             -id_params SEARCHGUI_IdentificationParameters.parameters
 
             -threads "\${GALAXY_SLOTS:-12}"
-            -correct_titles "${correct_titles}"
-            $missing_titles
-            -mgf_splitting "${mgf_splitting}"
-            -mgf_spectrum_count "${mgf_spectrum_count}"
+
+            #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
+                -correct_titles "${searchgui_advanced.correct_titles}"
+                $searchgui_advanced.missing_titles
+                -mgf_splitting "${searchgui_advanced.mgf_splitting}"
+                -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
+            #end if
 
             ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
             ## the tree is generated afterwards in PeptideShaker
@@ -111,54 +268,49 @@
 
             ##-makeblastdb_folder \$BLAST_ROOT_DIR
 
-            #if $advanced.advanced_type_selector == "advanced":
-
-                #if $advanced.xtandem.xtandem_selector == "yes"
-                    -xtandem 1
-                #else
-                    -xtandem 0
-                #end if
+            #set $engines_list = str($engines).split(',')
+            #if 'X!Tandem' in $engines_list:
+                -xtandem 1
+            #else
+                -xtandem 0
+            #end if
 
-                #if $advanced.omssa.omssa_selector == "yes"
-                    -omssa 1
-                #else
-                    -omssa 0
-                #end if
+            #if 'MyriMatch' in $engines_list:
+                -myrimatch 1
+            #else
+                -myrimatch 0
+            #end if
 
-                #if $advanced.msgf.msgf_selector == "yes"
-                    -msgf 1
-                #else
-                    -msgf 0
-                #end if
+            #if 'MSGF' in $engines_list:
+                -msgf 1
+            #else
+                -msgf 0
+            #end if
 
-                #if $advanced.myrimatch.myrimatch_selector == "yes"
-                    -myrimatch 1
-                #else
-                    -myrimatch 0
-                #end if
+            #if 'OMSSA' in $engines_list:
+                -omssa 1
+            #else
+                -omssa 0
+            #end if
 
-                #if $advanced.comet.comet_selector == "yes"
-                    -comet 1
-                #else
-                    -comet 0
-                #end if
+            #if 'Comet' in $engines_list:
+                -comet 1
+            #else
+                -comet 0
+            #end if
 
-                #if $advanced.ms_amanda.ms_amanda_selector == "yes"
-                    -ms_amanda 1
-                #else
-                    -ms_amanda 0
-                #end if
+            #if 'Tide' in $engines_list:
+                -tide 1
+            #else
+                -tide 0
+            #end if
 
-                #if $advanced.tide.tide_selector == "yes"
-                    -tide 1
-                #else
-                    -tide 0
-                #end if
+            #if 'MS_Amanda' in $engines_list:
+                -ms_amanda 1
+            #else
+                -ms_amanda 0
+            #end if
 
-            #else
-                -ms_amanda 0 -tide 0
-            #end if
-            
             ## single zip file
             -output_option 0
 
@@ -179,6 +331,7 @@
 ]]>
     </command>
     <inputs>
+
         <param format="fasta" name="input_database" type="data" label="Protein Database"
             help="Select FASTA database from history"/>
 
@@ -189,153 +342,539 @@
         <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
             help="Select appropriate MGF dataset(s) from history" />
 
-        <expand macro="general_options"/>
-
-        <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
-            help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
-            <option value="0">no correction</option>
-            <option value="1" selected="True">rename spectra</option>
-            <option value="2">delete spectra</option>
+        <!-- Search Engine Selection -->
+        <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
+            <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
+            <option value="X!Tandem" selected="True">X!Tandem</option>
+            <option value="MyriMatch">MyriMatch</option>
+            <option value="MS_Amanda">MS_Amanda</option> 
+            <option value="MSGF" selected="True">MS-GF+</option>
+            <option value="OMSSA" selected="True">OMSSA</option>
+            <option value="Comet">Comet</option>
+            <option value="Tide">Tide</option>
+            <validator type="no_options" message="Please select at least one output file" />
         </param>
 
-        <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
-            label="Add missing spectrum titles" help="(-missing_titles)"/>
 
-        <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
-            help="Choose a smaller value if you are running on a machine with limited memory"/>
+        <!-- General Parameters -->
+        <expand macro="general_options"/>
 
-        <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
-            help="Choose a smaller value if you are running on a machine with limited memory"/>
-
-        <conditional name="advanced">
-            <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
-                <option value="basic" selected="True">Basic</option>
+        <!-- Optional Advanced SearchGUI Parameters -->
+        <conditional name="searchgui_advanced">
+            <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
+                <option value="basic" selected="True">Default</option>
                 <option value="advanced">Advanced</option>
             </param>
             <when value="basic" />
             <when value="advanced">
-                <conditional name="xtandem">
-                    <param name="xtandem_selector" type="select" label="Run X!Tandem search">
-                        <option value="yes" selected="True">Search with X!Tandem</option>
-                        <option value="no">No X!Tandem search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                        <param name="xtandem_npeaks" type="integer" value="50" 
-                            label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
-                        <param name="xtandem_min_peaks" type="integer" value="15" 
-                            label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
-                        <param name="xtandem_min_frag_mz" type="integer" value="200" 
-                            label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
-                        <param name="xtandem_min_prec_mass" type="integer" value="200" 
-                            label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
-                        <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
-                            label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
+            <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
+                help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
+                <option value="0">no correction</option>
+                <option value="1" selected="True">rename spectra</option>
+                <option value="2">delete spectra</option>
+            </param>
+
+            <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
+                label="Add missing spectrum titles" help="(-missing_titles)"/>
+
+            <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
+                help="Choose a smaller value if you are running on a machine with limited memory"/>
+
+            <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
+                help="Choose a smaller value if you are running on a machine with limited memory"/>
+        </when>
+        </conditional>
+
 
-                        <conditional name="xtandem_refine"><!-- -xtandem_refine -->
-                            <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
-                                <option value="no" selected="True">Don't refine</option>
-                                <option value="yes" >Use refinement</option>
-                            </param>
-                            <when value="no"/>
-                            <when value="yes">
-                                <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0"
-                                    label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
-                                <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
-                                <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
-                                <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
-                                <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" 
-                                    label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
-                            </when>
-                        </conditional>
+        <!-- X!TANDEM ADVANCED PARAMETERS -->
+        <conditional name="xtandem">
+            <param name="xtandem_advanced" type="select" label="X!Tandem Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="xtandem_npeaks" type="integer" value="50" 
+                    label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
+                <param name="xtandem_min_peaks" type="integer" value="15" 
+                    label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
+                <param name="xtandem_min_frag_mz" type="integer" value="200" 
+                    label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
+                <param name="xtandem_min_prec_mass" type="integer" value="200" 
+                    label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
+                <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
+                    label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
+                <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
+                    label="X!Tandem: Dynamic Range" value="100" type="integer" />
+                <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
+                    label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
+                    label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 
+                <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
+                    label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 
+                <param name="xtandem_evalue" help="Highest value for recorded peptides"
+                    label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" />
+                <param name="xtandem_output_proteins" help="Controls output of protein sequences"
+                    label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                <param name="xtandem_output_sequences" help="Controls output of sequence information"
+                    label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                <param name="xtandem_output_spectra" help="Controls output of spectrum information"
+                    label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" />
+                <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
+                    
+                <conditional name="xtandem_refine"><!-- -xtandem_refine -->
+                    <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
+                        <option value="no" selected="True">Don't refine</option>
+                        <option value="yes" >Use refinement</option>
+                    </param>
+                    <when value="no"/>
+                    <when value="yes">
+                        <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
+                        <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                            label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
+                        <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                            label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
+                        <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
+                        <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                            label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
+                        <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                            label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
+                        <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
+                            label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
                     </when>
                 </conditional>
+            </when>
+        </conditional>
 
-                <conditional name="omssa">
-                    <param name="omssa_selector" type="select" label="Run OMSSA search">
-                        <option value="yes" selected="True">Search with OMSSA</option>
-                        <option value="no">No OMSSA search</option>
+        <!-- OMSSA ADVANCED PARAMETERS -->
+        <conditional name="omssa">
+            <param name="omssa_advanced" type="select" label="OMSSA Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
+                <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
+                <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
+                <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                
+                <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
+                  <!-- param name="omssa_isotopes" type="integer" value="0" 
+                      label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
+                   <param name="omssa_neutron" type="float" value="1446.94" 
+                       label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
+                <param name="omssa_low_intensity" type="float" value="0.0" 
+                    label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
+                <param name="omssa_high_intensity" type="float" value="0.2" 
+                    label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
+                   <param name="omssa_intensity_incr" type="float" value="0.0005" 
+                       label="OMSSA: Intensity Increment" help="Intensity increment" />
+                <param name="omssa_single_window_wd" type="integer" value="27" 
+                    label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
+                <param name="omssa_double_window_wd" type="integer" value="14" 
+                    label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
+                <param name="omssa_single_window_pk" type="integer" value="2" 
+                    label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
+                <param name="omssa_double_window_pk" type="integer" value="2" 
+                    label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
+                <param name="omssa_min_ann_int_pks" type="integer" value="6" 
+                    label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
+                <param name="omssa_min_annotated_peaks" type="integer" value="2" 
+                    label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
+                   <param name="omssa_min_peaks" type="integer" value="4" 
+                       label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
+                <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
+                <param name="omssa_max_ladders" type="integer" value="128" 
+                    label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
+                <param name="omssa_max_frag_charge" type="integer" value="2" 
+                    label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
+                <param name="omssa_fraction" type="float" value="0.95" 
+                    label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
+                <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+                    label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
+                <param name="omssa_charge" type="select" 
+                    label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
+                    <option value="0" >Minus</option>
+                    <option value="1" selected="True">Plus</option>
+                </param>
+                <param name="omssa_prec_per_spectrum" type="integer" value="1" 
+                    label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
+                <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+                    label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
+                <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"  
+                    label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
+                <param name="omssa_max_frag_series" type="integer" value="100" 
+                    label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
+                <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+                    label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
+                <param name="omssa_consecutive_p" type="float" value="0.5" 
+                    label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
+                <param name="omssa_it_sequence_evalue" type="float" value="0.0" 
+                    label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
+                <param name="omssa_it_spectrum_evalue" type="float" value="0.01" 
+                    label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
+                <param name="omssa_it_replace_evalue" type="float" value="0.01" 
+                    label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
+                <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+                    label="OMSSA: Remove Precursor" help="Remove precursors" />
+                <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"  
+                    label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
+                <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"  
+                    label="OMSSA: Remove Precursor" help="Remove precursors" />
+                <param name="omssa_max_evalue" type="float" value="100" 
+                    label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
+                <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"  
+                    label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
+                <param name="omssa_it_replace_evalue" type="float" value="100" 
+                    label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
+                <param name="omssa_hitlist_length" type="integer" value="0" 
+                    label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
+                <param name="omssa_hitlist_charge" type="integer" value="30" 
+                    label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
+                <param name="omssa_min_pep_length" type="integer" value="4" 
+                    label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
+                <param name="omssa_max_pep_length" type="integer" value="40" 
+                    label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
+                <param name="omssa_format" label="OMSSA output format" type="select" >
+                    <option value="0" selected="True">OMX</option>
+                    <option value="1" >CSV</option>
+                </param>
+            </when>
+        </conditional>
+
+        <!-- MS-GF+ ADVANCED PARAMETERS -->
+        <conditional name="msgf">
+            <param name="msgf_advanced" type="select" label="MSGF Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
+                <param name="msgf_min_pep_length" type="integer" value="6"
+                    label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
+                <param name="msgf_max_pep_length" type="integer" value="30" 
+                    label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
+                <param name="msgf_termini" type="select" format="text" 
+                    label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
+                    <option value="0">0 (ie non-specific cleavage)</option>
+                    <option value="1">1 (ie semi-tryptic cleavage)</option>
+                    <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
+                </param>
+                <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
+                
+                <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
+                    <option value="0" selected="True">Low-res LCQ/LTQ</option>
+                    <option value="1" >High-res LTQ</option>
+                    <option value="2" >TOF</option>
+                    <option value="3" >Q-Exactive</option>
+                </param>
+                <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
+                    <option value="0" selected="True">As written in the spectrum or CID if no info</option>
+                    <option value="1" >CID</option>
+                    <option value="2" >ETD</option>
+                    <option value="3" >HCD</option>
+                </param>
+                <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples">
+                    <option value="0" selected="True">Automatic</option>
+                    <option value="1" >Phosphorylation</option>
+                    <option value="2" >iTRAQ</option>
+                    <option value="3" >iTRAQPhospho</option>
+                    <option value="4" >TMT</option>
+                    <option value="5" >Standard</option>
+                </param>
+                <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
+                <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
+                    <option value="0" selected="True">output basic scores only</option>
+                    <option value="1" >output additional features</option>
+                </param>
+                <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
+                <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> 
+            </when>
+        </conditional>
+
+          <!-- MS-AMANDA ADVANCED PARAMETERS  -->
+        <conditional name="ms_amanda">
+            <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="ms_amanda_decoy"  type="boolean" truevalue="1" falsevalue="0" checked="false" 
+                    label="MS Amanda: Generate Decoys" help="generate decoys" />
+                <param name="ms_amanda_max_evalue" type="float" value="100" 
+                    label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" />
+                <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." />
+                <param name="ms_amanda_max_rank" type="integer" value="5" 
+                    label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
+                <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
+            </when>
+        </conditional>
+
+
+        <!-- TIDE ADVANCED PARAMETERS -->
+        <conditional name="tide">
+            <param name="tide_advanced" type="select" label="TIDE Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="tide_num_ptms" type="integer" value="100"
+                    label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
+                <param name="tide_num_ptms_per_type" type="integer" value="2"
+                    label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
+                <param name="tide_min_pep_length" type="integer" value="6"
+                    label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
+                <param name="tide_max_pep_length" type="integer" value="30"
+                    label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
+                <param name="tide_min_prec_mass" type="float" value="200.0"
+                    label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
+                <param name="tide_max_prec_mass" type="float" value="7200.0"
+                    label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
+                <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
+                    <option value="none" selected="True">none</option>
+                    <option value="shuffle" >shuffle</option>
+                    <option value="peptide-revers" >peptide-reverse</option>
+                    <option value="protein-reverse" >protein-reverse</option>
+                </param>
+                <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
+                    <option value="N" >N</option>
+                    <option value="C" >C</option>
+                    <option value="NC" selected="True">NC</option>
+                    <option value="non" >none</option>
+                </param>
+                <param name="tide_decoy_seed" type="integer" value="1"
+                    label="TIDE: Decoy Seed" help="Set the decoy seed"/>
+                <param name="tide_output_folder" type="text" value="crux-output"
+                    label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
+                <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
+                <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
+                    <option value="0" >0</option>
+                    <option value="10" >10</option>
+                    <option value="20" >20</option>
+                    <option value="30" selected="True">30</option>
+                    <option value="40" >40</option>
+                    <option value="50" >50</option>
+                    <option value="60" >60</option>
+                </param>
+
+                <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
+                <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
+                <param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules">
+                    <option value="full-digest" selected="True">full-digest</option>
+                    <option value="partial-digest" >partial-digest</option>
+                </param>
+                <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
+                <param name="tide_max_psms" type="integer" value="10"
+                    label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
+                <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
+                <param name="tide_min_spectrum_mz" type="float" value="0.0"
+                    label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
+                <param name="tide_max_spectrum_mz" type="float" value="100000.0"
+                    label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
+                <param name="tide_min_spectrum_peaks" type="integer" value="20"
+                    label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
+                <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
+                    <option value="1" >1</option>
+                    <option value="2" >2</option>
+                    <option value="3" >3</option>
+                    <option value="all" selected="True">all</option>
+                </param>
+                <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
+                <param name="tide_remove_prec_tol" type="float" value="1.5"
+                    label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
+                <param name="tide_progress_indicator" type="integer" value="1000"
+                    label="TIDE: Progress Indicator" help="Choose the progress indicator frequency  (in number of fragmentation spectra processed)"/>
+                <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
+                <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
+                <param name="tide_mz_bin_width" type="float" value="0.02"
+                    label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
+                <param name="tide_mz_bin_offset" type="float" value="0.0"
+                    label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
+                <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
+                <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
+                <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
+                <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
+                <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
+                <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
+                    label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
+                <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
+                    label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
+            </when>
+        </conditional>
+
+        <!-- MyriMatch ADVANCED PARAMETERS -->
+        <conditional name="myrimatch">
+            <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="myrimatch_min_pep_length"  type="integer" value="6"
+                    label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
+                <param name="myrimatch_max_pep_length"  type="integer" value="30"
+                    label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
+                <param name="myrimatch_min_prec_mass"  type="float" value="0.0"
+                    label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
+                <param name="myrimatch_max_prec_mass"  type="float" value="10000.0"
+                    label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
+                <param name="myrimatch_isotope_low"  type="integer" value="-1"
+                    label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
+                <param name="myrimatch_isotope_high"  type="integer" value="2"
+                    label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
+                <param name="myrimatch_num_matches"  type="integer" value="10"
+                    label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
+                <param name="myrimatch_num_ptms"  type="integer" value="2"
+                    label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" />
+                <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
+                    <option value="CID" selected="True">CID</option>
+                    <option value="ETD" >ETD</option>
+                </param>
+                <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">
+                    <option value="0">non-tryptic</option>
+                    <option value="1" >semi-tryptic</option>
+                    <option value="2"  selected="True" >fully-tryptic</option>
+                </param>
+                <param name="myrimatch_plus_three"  type="boolean" truevalue="1" falsevalue="0" checked="true" 
+                    label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
+                <param name="myrimatch_xcorr"  type="boolean" truevalue="1" falsevalue="0" checked="false" 
+                    label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />                        
+                <param name="myrimatch_tic_cutoff"  type="float" value="0.98"
+                    label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" />
+                <param name="myrimatch_intensity_classes"  type="integer" value="3"
+                    label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
+                <param name="myrimatch_class_multiplier"  type="integer" value="2"
+                    label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
+                <param name="myrimatch_num_batches"  type="integer" value="50"
+                    label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
+                <param name="myrimatch_max_peak"  type="integer" value="100"
+                    label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
+            </when>
+        </conditional>
+
+        <!-- Comet ADVANCED PARAMETERS -->
+        <conditional name="comet">
+            <param name="comet_advanced" type="select" label="Comet Options">
+                <option value="yes">Advanced</option>
+                <option value="no" selected="True">Default</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <!-- Spectrum Related parameters -->
+                <conditional name="comet_spectrum">
+                    <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
+                        <option value="yes">Set Spectrum Parameters</option>
+                        <option value="no" selected="True">Keep Default Spectrum Parameters</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
-                        <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
-                        <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
-                        <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
+                        <param name="comet_min_peaks"  type="integer" value="10"
+                            label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
+                        <param name="comet_min_peak_int"  type="float" value="0.0"
+                            label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
+                        <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
+                            <option value="0"  selected="True" >off</option>
+                            <option value="1">on</option>
+                            <option value="2">as expected for ETD/ECD spectra</option>
+                        </param>
+                        <when value="0" />
+                        <when value="1">
+                            <param name="comet_remove_prec_tol"  type="float" value="1.5"
+                                label="Comet: Remove Precursor Tolerance" />
+                        </when>
+                        <when value="2">
+                            <param name="comet_remove_prec_tol"  type="float" value="1.5"
+                                label="Comet: Remove Precursor Tolerance" />
+                        </when>
+                        <param name="comet_clear_mz_range_lower"  type="float" value="0.0"
+                            label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
+                        <param name="comet_clear_mz_range_upper"  type="float" value="0.0"
+                            label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />    
                     </when>
                 </conditional>
-
-                <conditional name="msgf">
-                    <param name="msgf_selector" type="select" label="Run MSGF search">
-                        <option value="yes" selected="True">Search with MSGF</option>
-                        <option value="no">No MSGF search</option>
+                  <!-- Search Related parameters -->
+                <conditional name="comet_search">
+                    <param name="comet_search_selector" type="select" label="Comet: Search Related">
+                        <option value="yes">Set Search Parameters</option>
+                        <option value="no" selected="True">Keep Default Search Parameters</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                        <param name="msgf_min_pep_length" type="integer" value="6"
-                            label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
-                        <param name="msgf_max_pep_length" type="integer" value="30" 
-                            label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
-                        <param name="msgf_termini" type="select" format="text" 
-                            label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
-                            <option value="0">0 (ie non-specific cleavage)</option>
-                            <option value="1">1 (ie semi-tryptic cleavage)</option>
-                            <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
+                        <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
+                            <option value="1">semi-specific</option>
+                            <option value="2" selected="True">full-enzyme</option>
+                            <option value="8">unspecific N-term</option>
+                            <option value="9">unspecific C-term</option>
+                        </param>
+                        <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement">
+                            <option value="0" selected="True">off</option>
+                            <option value="1">-1,0,+1,+2,+3</option>
+                            <option value="2">-8,-4,0,+4,+8</option>
                         </param>
-                        <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
+                        <param name="comet_min_prec_mass"  type="float" value="0.0"
+                            label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
+                        <param name="comet_max_prec_mass"  type="float" value="10000.0"
+                            label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
+                        <param name="comet_num_matches"  type="integer" value="10"
+                            label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
+                        <param name="comet_max_frag_charge"  type="integer" value="3"
+                            label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
+                        <param name="comet_remove_meth"  type="boolean" truevalue="1" falsevalue="0" checked="false" 
+                            label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
+                        <param name="comet_batch_size"  type="integer" value="0"
+                            label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" />
+                        <param name="comet_num_ptms"  type="integer" value="10"
+                            label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />    
                     </when>
                 </conditional>
-
-                <conditional name="myrimatch">
-                    <param name="myrimatch_selector" type="select" label="Run MyriMatch search">
-                        <option value="yes" selected="True">Search with MyriMatch</option>
-                        <option value="no">No MyriMatch search</option>
+                <!-- Fragment Ions Related parameters -->
+                <conditional name="comet_fragment_ions">
+                    <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
+                        <option value="yes">Set Fragment Ions Parameters</option>
+                        <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
                     </param>
                     <when value="no" />
                     <when value="yes">
-                    </when>
-                </conditional>
-
-                <conditional name="comet">
-                    <param name="comet_selector" type="select" label="Run Comet search">
-                        <option value="yes"  selected="True">Search with Comet</option>
-                        <option value="no">No Comet search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
+                        <param name="comet_frag_bin_offset"  type="float" value="0.4"
+                            label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
+                        <param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true" 
+                            label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />
+                        <param name="comet_theoretical_fragment_ions"  type="integer" value="0"
+                            label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />                                
                     </when>
                 </conditional>
-
-                <conditional name="ms_amanda">
-                    <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
-                        <option value="yes">Search with MS Amanda</option>
-                        <option value="no" selected="True">No MS Amanda search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                    </when>
-                </conditional>
-
-                <conditional name="tide">
-                    <param name="tide_selector" type="select" label="Run Tide search">
-                        <option value="yes">Search with Tide</option>
-                        <option value="no" selected="True">No Comet search</option>
-                    </param>
-                    <when value="no" />
-                    <when value="yes">
-                    </when>
-                </conditional>
-
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
+        <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
     </outputs>
     <tests>
+
+        <!-- Test that specifying non-default search engines works -->
         <test>
             <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
             <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
@@ -344,21 +883,35 @@
             <param name="variable_modifications" value="oxidation of m"/>
             <param name="min_charge" value="1"/>
             <param name="max_charge" value="3"/>
-            <param name="advanced_type_selector" value="advanced"/>
-            <param name="xtandem_selector" value="yes"/>
-            <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
-            <param name="omssa_selector" value="no"/>
-            <param name="msgf_selector" value="yes"/>
-            <param name="ms_amanda_selector" value="no"/>
-            <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" /> 
+            <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
+            <param name="xtandem.xtandem_advanced" value="yes"/>
+            <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
+
+            <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> 
         </test>
+
+        <!-- Test that search works with MSAmanda -->
+        <test>
+            <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
+            <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
+            <param name="precursor_ion_tol" value="100"/>
+            <param name="fixed_modifications" value="carbamidomethyl c"/>
+            <param name="variable_modifications" value="oxidation of m"/>
+            <param name="min_charge" value="1"/>
+            <param name="max_charge" value="3"/>
+            <param name="engines" value="MS_Amanda"/>
+
+            <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="600" /> 
+        </test>
+
+
     </tests>
     <help>
 **What it does**
 
 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
-
-By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run.
+Default:     X! Tandem, OMSSA and MS-GF+ are executed.
+Optional:     MyriMatch, MS-Amanda, Comet and Tide can be executed.
 
     </help>
     <expand macro="citations" />
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_certificate_result2.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/peptide_shaker_certificate_result2.txt	Tue Jun 16 23:43:39 2015 -0400
@@ -0,0 +1,67 @@
+Project Details1: PeptideShaker Version: 0.39.1
+2: Date: Thu Jun 04 20:07:16 CEST 2015
+3: Experiment: Galaxy_Experiment_2015060420071433441234
+4: Sample: Sample_2015060420071433441234
+5: Replicate Number: 1
+6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet
+Database Search Parameters
+
+1: Precursor Accuracy Unit: ppm
+2: Precursor Ion m/z Tolerance: 100.0
+3: Fragment Ion m/z Tolerance: 0.5
+4: Enzyme: Trypsin
+5: Number of Missed Cleavages: Not implemented
+6: Database: input_database.fasta
+7: Forward Ion: b
+8: Rewind Ion: y
+9: Fixed Modifications: carbamidomethyl c
+10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q
+11: Refinement Variable Modifications: 
+12: Refinement Fixed Modifications: 
+Input Filters
+
+1: Minimal Peptide Length: 1
+2: Maximal Peptide Length: 30
+3: Precursor m/z Tolerance: 10.0
+4: Precursor m/z Tolerance Unit: Yes
+5: Unrecognized Modifications Discarded: No
+Validation Summary
+
+1: #Validated Proteins: 0.0
+2: Protein Total: 0.0
+3Protein FDR Limit: 1.0 %
+4: Protein FNR Limit: 0.0 %
+5: Protein Confidence Limit: -1.0 %
+6: Protein PEP Limit: 101.0 %
+7: Protein Confidence Accuracy: 0.0 %
+8: #Validated Peptides: 0.0
+9: Peptide Total: 0.0
+10: Peptide FDR Limit: 1.0 %
+11: Peptide FNR Limit: 0.0 %
+12: Peptide Confidence Limit: -1.0 %
+13: Peptide PEP Limit: 101.0 %
+14: Peptide Confidence Accuracy: 0.0 %
+15: #Validated PSM: 0.0
+16: PSM Total: 0.0
+17: PSM FDR Limit: 1.0 %
+18: PSM FNR Limit: 0.0 %
+19: PSM Confidence Limit: -1.0 %
+20: PSM PEP Limit: 101.0 %
+21: PSM Confidence Accuracy: 0.0 %
+Postranslational Modification Scoring Settings
+
+1: A-score: No
+2: Accounting for Neutral Losses: No
+3: False Location Rate: 1.0
+Spectrum Counting Parameters
+
+1: Method: NSAF
+2: Validated Matches Only: Yes
+Annotation Settings
+
+1: Intensity Limit: 0.75
+2: Automatic Annotation: Yes
+3: Selected Ions: b, y
+4: Neutral Losses: H2O, NH3
+5: Neutral Losses Sequence Dependence: Yes
+6: Fragment Ion m/z Tolerance: 0.5
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_hierarchical_result2.tabular
--- a/test-data/peptide_shaker_hierarchical_result2.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_hierarchical_result2.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,78 +1,79 @@
-	Main Accession	Description	MW [kDa]	Coverage [%]	Possible Coverage [%]	Spectrum Counting NSAF 	Confidently Localized Modification Sites	# Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	PI	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67		69.88215372568374	3757.96	92.52	0.014450915311500504					Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	39	39	100.0	0	Doubtful
+	Main Accession	Description	MW [kDa]	Possible Coverage [%]	Coverage [%]	Spectrum Counting NSAF 	Confidently Localized Modification Sites	# Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	PI	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67		69.88215372568374	92.52	37.58	0.01785479771710408					Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	40	40	100.0	0	Doubtful
 	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
-1.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN				2	2	100.0	0	Doubtful
+1.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS				4	4	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.1.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH			tinyspectra.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
-1.1.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH			tinyspectra.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
-1.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	AK; AK	IS; IS				4	4	100.0	0	Doubtful
+1.1.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
+1.1.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
+1.1.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
+1.1.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			searchgui_tinyspectra1.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
+1.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE				4	4	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.2.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			tinyspectra.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
-1.2.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			tinyspectra.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
-1.2.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			tinyspectra.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
-1.2.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH			tinyspectra.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
-1.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK				2	2	100.0	0	Doubtful
+1.2.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
+1.2.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
+1.2.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
+1.2.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			searchgui_tinyspectra1.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
+1.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.3.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH			tinyspectra.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
-1.3.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH			tinyspectra.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
-1.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	AR; AR	LI; LI				2	2	100.0	0	Doubtful
+1.3.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
+1.3.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH			searchgui_tinyspectra1.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
+1.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.4.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH			tinyspectra.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
-1.4.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH			tinyspectra.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
-1.5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN				2	2	100.0	0	Doubtful
+1.4.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
+1.4.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			searchgui_tinyspectra1.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
+1.5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	LK; LK	IN; IN				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.5.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH			tinyspectra.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
-1.5.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH			tinyspectra.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
-1.6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS				3	3	100.0	0	Doubtful
+1.5.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
+1.5.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH			searchgui_tinyspectra1.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
+1.6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV				4	4	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.6.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			tinyspectra.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
-1.6.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			tinyspectra.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
-1.6.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			tinyspectra.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
-1.7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS				2	2	100.0	0	Doubtful
-	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.7.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH			tinyspectra.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
-1.7.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH			tinyspectra.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
-1.8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	QK; QK	SV; SV				4	4	100.0	0	Doubtful
+1.6.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
+1.6.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
+1.6.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
+1.6.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			searchgui_tinyspectra1.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
+1.7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	VR; VR	LK; LK				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.8.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			tinyspectra.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
-1.8.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			tinyspectra.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
-1.8.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			tinyspectra.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
-1.8.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH			tinyspectra.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
-1.9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	RR; RR	AS; AS				2	2	100.0	0	Doubtful
+1.7.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
+1.7.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH			searchgui_tinyspectra1.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
+1.8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NK; NK	LS; LS				4	4	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.9.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			tinyspectra.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
-1.9.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH			tinyspectra.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
-1.10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NR; NR	SE; SE				4	4	100.0	0	Doubtful
+1.8.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
+1.8.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
+1.8.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
+1.8.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH			searchgui_tinyspectra1.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
+1.9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.10.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			tinyspectra.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
-1.10.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			tinyspectra.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
-1.10.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			tinyspectra.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
-1.10.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH			tinyspectra.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
-1.11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	RR; RR	NL; NL				2	2	100.0	0	Doubtful
+1.9.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
+1.9.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH			searchgui_tinyspectra1.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
+1.10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM				2	2	100.0	0	Doubtful
+	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
+1.10.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+1.10.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH			searchgui_tinyspectra1.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+1.11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	AR; AR	QS; QS				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.11.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH			tinyspectra.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
-1.11.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH			tinyspectra.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
-1.12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	GR; GR	DM; DM				2	2	100.0	0	Doubtful
+1.11.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
+1.11.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH			searchgui_tinyspectra1.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
+1.12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	MK; MK	SN; SN				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.12.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH			tinyspectra.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
-1.12.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH			tinyspectra.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
-1.13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS				2	2	100.0	0	Doubtful
+1.12.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
+1.12.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH			searchgui_tinyspectra1.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
+1.13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID				4	4	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.13.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH			tinyspectra.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
-1.13.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH			tinyspectra.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
-1.14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	DR; DR; DR	ID; ID; ID				4	4	100.0	0	Doubtful
+1.13.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
+1.13.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
+1.13.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
+1.13.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			searchgui_tinyspectra1.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
+1.14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.14.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			tinyspectra.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
-1.14.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			tinyspectra.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
-1.14.3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			tinyspectra.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
-1.14.4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH			tinyspectra.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
-1.15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	SK; SK; SK	SK; SK; SK				2	2	100.0	0	Doubtful
+1.14.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
+1.14.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			searchgui_tinyspectra1.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
+1.15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	AK; AK; AK	NS; NS; NS				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1.15.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			tinyspectra.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
-1.15.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH			tinyspectra.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91		69.9696370486838	325.2	100.0	0.0032520325203252032					Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	2	2	100.0	0	Doubtful
+1.15.1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
+1.15.2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH			searchgui_tinyspectra1.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
+2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91		69.9696370486838	100.0	3.25	0.0032520325203252032					Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
 2.1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	MR; MR	YQ; YQ				2	2	100.0	0	Doubtful
 	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-2.1.1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH			tinyspectra.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
-2.1.2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH			tinyspectra.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
+2.1.1	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
+2.1.2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH			searchgui_tinyspectra1.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_peptides_phoshorylation_result2.tabular
--- a/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_peptides_phoshorylation_result2.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,17 +1,17 @@
 	Protein(s)	Sequence	Modified Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	LK; LK	IN; IN								2	2	100.0	0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	MR; MR	YQ; YQ								2	2	100.0	0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	AK; AK	IS; IS								4	4	100.0	0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH	VR; VR	LK; LK								2	2	100.0	0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	AR; AR	LI; LI								2	2	100.0	0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	MK; MK	SN; SN								2	2	100.0	0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	NK; NK	LS; LS								3	3	100.0	0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH	AR; AR	QS; QS								2	2	100.0	0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	QK; QK	SV; SV								4	4	100.0	0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	AK; AK; AK	NS; NS; NS								2	2	100.0	0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH	DR; DR; DR	ID; ID; ID								4	4	100.0	0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	RR; RR	AS; AS								2	2	100.0	0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	NR; NR	SE; SE								4	4	100.0	0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	RR; RR	NL; NL								2	2	100.0	0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	SK; SK; SK	SK; SK; SK								2	2	100.0	0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	GR; GR	DM; DM								2	2	100.0	0	Doubtful
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	AK; AK	IS; IS								4	4	100.0	0	Doubtful
+2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	NR; NR	SE; SE								4	4	100.0	0	Doubtful
+3	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	MR; MR	YQ; YQ								2	2	100.0	0	Doubtful
+4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	AR; AR	LI; LI								2	2	100.0	0	Doubtful
+5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	RR; RR	AS; AS								2	2	100.0	0	Doubtful
+6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH	DR; DR; DR	ID; ID; ID								4	4	100.0	0	Doubtful
+7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	LK; LK	IN; IN								2	2	100.0	0	Doubtful
+8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	QK; QK	SV; SV								4	4	100.0	0	Doubtful
+9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	SK; SK; SK	SK; SK; SK								2	2	100.0	0	Doubtful
+10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH	VR; VR	LK; LK								2	2	100.0	0	Doubtful
+11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	NK; NK	LS; LS								4	4	100.0	0	Doubtful
+12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	AK; AK; AK	NS; NS; NS								2	2	100.0	0	Doubtful
+13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	RR; RR	NL; NL								2	2	100.0	0	Doubtful
+14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	GR; GR	DM; DM								2	2	100.0	0	Doubtful
+15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH	AR; AR	QS; QS								2	2	100.0	0	Doubtful
+16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	MK; MK	SN; SN								2	2	100.0	0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_peptides_result2.tabular
--- a/test-data/peptide_shaker_peptides_result2.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_peptides_result2.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,17 +1,17 @@
 	Protein(s)	Sequence	Modified Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	LK; LK	IN; IN				2	2	100.0	0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	MR; MR	YQ; YQ				2	2	100.0	0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	AK; AK	IS; IS				4	4	100.0	0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH	VR; VR	LK; LK				2	2	100.0	0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	AR; AR	LI; LI				2	2	100.0	0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	MK; MK	SN; SN				2	2	100.0	0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	NK; NK	LS; LS				3	3	100.0	0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH	AR; AR	QS; QS				2	2	100.0	0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	QK; QK	SV; SV				4	4	100.0	0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	AK; AK; AK	NS; NS; NS				2	2	100.0	0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH	DR; DR; DR	ID; ID; ID				4	4	100.0	0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	RR; RR	AS; AS				2	2	100.0	0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	NR; NR	SE; SE				4	4	100.0	0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	RR; RR	NL; NL				2	2	100.0	0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	SK; SK; SK	SK; SK; SK				2	2	100.0	0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	GR; GR	DM; DM				2	2	100.0	0	Doubtful
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	AK; AK	IS; IS				4	4	100.0	0	Doubtful
+2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	NR; NR	SE; SE				4	4	100.0	0	Doubtful
+3	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	MR; MR	YQ; YQ				2	2	100.0	0	Doubtful
+4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	AR; AR	LI; LI				2	2	100.0	0	Doubtful
+5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	RR; RR	AS; AS				2	2	100.0	0	Doubtful
+6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH	DR; DR; DR	ID; ID; ID				4	4	100.0	0	Doubtful
+7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	LK; LK	IN; IN				2	2	100.0	0	Doubtful
+8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	QK; QK	SV; SV				4	4	100.0	0	Doubtful
+9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	SK; SK; SK	SK; SK; SK				2	2	100.0	0	Doubtful
+10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH	VR; VR	LK; LK				2	2	100.0	0	Doubtful
+11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	NK; NK	LS; LS				4	4	100.0	0	Doubtful
+12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	AK; AK; AK	NS; NS; NS				2	2	100.0	0	Doubtful
+13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	RR; RR	NL; NL				2	2	100.0	0	Doubtful
+14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	GR; GR	DM; DM				2	2	100.0	0	Doubtful
+15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH	AR; AR	QS; QS				2	2	100.0	0	Doubtful
+16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	MK; MK	SN; SN				2	2	100.0	0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_peptides_result3.tabular
--- a/test-data/peptide_shaker_peptides_result3.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_peptides_result3.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -0,0 +1,17 @@
+	Protein(s)	Sequence	Modified Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK	NH2-NLLLDANKENGELK-COOH	AK; AK	IS; IS				4	4	100.0	0	Doubtful
+2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR	NH2-ISTGYITENIGGFR-COOH	NR; NR	SE; SE				4	4	100.0	0	Doubtful
+3	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91; cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK	NH2-EIRDEYDNQLNLLSADLESK-COOH	MR; MR	YQ; YQ				2	2	100.0	0	Doubtful
+4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK	NH2-INEDRIDELQDKVNK-COOH	AR; AR	LI; LI				2	2	100.0	0	Doubtful
+5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR	NH2-SHVVGAGLGGGSMGSMNQSMSLHGGR-COOH	RR; RR	AS; AS				2	2	100.0	0	Doubtful
+6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK	NH2-LISATSISPEHK-COOH	DR; DR; DR	ID; ID; ID				4	4	100.0	0	Doubtful
+7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR	NH2-ISITTYEEEIEDLHATAR-COOH	LK; LK	IN; IN				2	2	100.0	0	Doubtful
+8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR	NH2-VGNLEEELEFLR-COOH	QK; QK	SV; SV				4	4	100.0	0	Doubtful
+9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR	NH2-SVISIGEVESEGQYVTLENTSSGR-COOH	SK; SK; SK	SK; SK; SK				2	2	100.0	0	Doubtful
+10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR	NH2-SLQAENEQLR-COOH	VR; VR	LK; LK				2	2	100.0	0	Doubtful
+11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK	NH2-LHVEMESMIEELQMLMDAK-COOH	NK; NK	LS; LS				4	4	100.0	0	Doubtful
+12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67; cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR	NH2-KGDIIATVDEWGPVNR-COOH	AK; AK; AK	NS; NS; NS				2	2	100.0	0	Doubtful
+13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK	NH2-EFDVEPLKEAYQAEIDEAK-COOH	RR; RR	NL; NL				2	2	100.0	0	Doubtful
+14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK	NH2-ASLGMAAGVAGGIATK-COOH	GR; GR	DM; DM				2	2	100.0	0	Doubtful
+15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR	NH2-YESQLSQIR-COOH	AR; AR	QS; QS				2	2	100.0	0	Doubtful
+16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67; cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR	NH2-MEIITITNQLQR-COOH	MK; MK	SN; SN				2	2	100.0	0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_proteins_phoshorylation_result2.tabular
--- a/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_proteins_phoshorylation_result2.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,3 +1,3 @@
-	Main Accession	Description	Gene Name	Chromosome	MW [kDa]	Coverage [%]	Possible Coverage [%]	Spectrum Counting NSAF 	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	PI	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67				69.88215372568374	3757.96	92.52	0.014450915311500504		0		0	Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	39	39	100.0	0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91				69.9696370486838	325.2	100.0	0.0032520325203252032		0		0	Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	2	2	100.0	0	Doubtful
+	Main Accession	Description	Gene Name	Chromosome	MW [kDa]	Possible Coverage [%]	Coverage [%]	Spectrum Counting NSAF 	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	PI	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67				69.88215372568374	92.52	37.58	0.01785479771710408		0		0	Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	40	40	100.0	0	Doubtful
+2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91				69.9696370486838	100.0	3.25	0.0032520325203252032		0		0	Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	2	2	100.0	0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_proteins_result2.tabular
--- a/test-data/peptide_shaker_proteins_result2.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_proteins_result2.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,3 +1,3 @@
-	Main Accession	Description	Gene Name	Chromosome	MW [kDa]	Coverage [%]	Possible Coverage [%]	Spectrum Counting NSAF 	Confidently Localized Modification Sites	# Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	PI	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67				69.88215372568374	3757.96	92.52	0.014450915311500504					Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	39	39	100.0	0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91				69.9696370486838	325.2	100.0	0.0032520325203252032					Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	2	2	100.0	0	Doubtful
+	Main Accession	Description	Gene Name	Chromosome	MW [kDa]	Possible Coverage [%]	Coverage [%]	Spectrum Counting NSAF 	Confidently Localized Modification Sites	# Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	PI	Secondary Accessions	Protein Group	#Validated Peptides	#Peptides	#Unique	#Validated PSMs	#PSMs	Confidence	Decoy	Validation
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67				69.88215372568374	92.52	37.58	0.01785479771710408					Related Proteins	cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	15	15	15	40	40	100.0	0	Doubtful
+2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91				69.9696370486838	100.0	3.25	0.0032520325203252032					Related Proteins	cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	1	1	1	2	2	100.0	0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_psm_phoshorylation_result2.tabular
--- a/test-data/peptide_shaker_psm_phoshorylation_result2.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_psm_phoshorylation_result2.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,42 +1,43 @@
 	Protein(s)	Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confident Phosphosites	#Confident Phosphosites	Ambiguous Phosphosites	#Ambiguous Phosphosites	Confidence	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			tinyspectra.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0								100.0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			tinyspectra.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0								100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0								100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			tinyspectra.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0								100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			tinyspectra.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0								100.0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			tinyspectra.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0								100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0								100.0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			tinyspectra.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0								100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0								100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0								100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0								100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			tinyspectra.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0								100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0								100.0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0								100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			tinyspectra.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0								100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0								100.0	Doubtful
-17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			tinyspectra.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0								100.0	Doubtful
-18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0								100.0	Doubtful
-19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0								100.0	Doubtful
-20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			tinyspectra.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0								100.0	Doubtful
-21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			tinyspectra.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0								100.0	Doubtful
-22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			tinyspectra.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0								100.0	Doubtful
-23	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			tinyspectra.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0								100.0	Doubtful
-24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0								100.0	Doubtful
-25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			tinyspectra.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0								100.0	Doubtful
-26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			tinyspectra.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0								100.0	Doubtful
-27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			tinyspectra.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0								100.0	Doubtful
-28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0								100.0	Doubtful
-29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0								100.0	Doubtful
-30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0								100.0	Doubtful
-31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			tinyspectra.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0								100.0	Doubtful
-32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			tinyspectra.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0								100.0	Doubtful
-33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0								100.0	Doubtful
-34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0								100.0	Doubtful
-35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0								100.0	Doubtful
-36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0								100.0	Doubtful
-37	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			tinyspectra.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0								100.0	Doubtful
-38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			tinyspectra.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0								100.0	Doubtful
-39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0								100.0	Doubtful
-40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			tinyspectra.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0								100.0	Doubtful
-41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			tinyspectra.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0								100.0	Doubtful
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0								100.0	Doubtful
+2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0								100.0	Doubtful
+3	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0								100.0	Doubtful
+4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0								100.0	Doubtful
+5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0								100.0	Doubtful
+6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0								100.0	Doubtful
+7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0								100.0	Doubtful
+8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0								100.0	Doubtful
+9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0								100.0	Doubtful
+10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0								100.0	Doubtful
+11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0								100.0	Doubtful
+12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0								100.0	Doubtful
+13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0								100.0	Doubtful
+14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0								100.0	Doubtful
+15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0								100.0	Doubtful
+16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0								100.0	Doubtful
+17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0								100.0	Doubtful
+18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0								100.0	Doubtful
+19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0								100.0	Doubtful
+20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0								100.0	Doubtful
+21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0								100.0	Doubtful
+22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0								100.0	Doubtful
+23	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0								100.0	Doubtful
+24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0								100.0	Doubtful
+25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0								100.0	Doubtful
+26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0								100.0	Doubtful
+27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0								100.0	Doubtful
+28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0								100.0	Doubtful
+29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0								100.0	Doubtful
+30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0								100.0	Doubtful
+31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0								100.0	Doubtful
+32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0								100.0	Doubtful
+33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0								100.0	Doubtful
+34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0								100.0	Doubtful
+35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0								100.0	Doubtful
+36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0								100.0	Doubtful
+37	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0								100.0	Doubtful
+38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0								100.0	Doubtful
+39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0								100.0	Doubtful
+40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0								100.0	Doubtful
+41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0								100.0	Doubtful
+42	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0								100.0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_psm_result1.tabular
--- a/test-data/peptide_shaker_psm_result1.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_psm_result1.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,42 +1,43 @@
 	Protein(s)	Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			tinyspectra.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			tinyspectra.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			tinyspectra.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			tinyspectra.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			tinyspectra.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			tinyspectra.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			tinyspectra.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			tinyspectra.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
-17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			tinyspectra.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
-18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
-19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
-20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			tinyspectra.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
-21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			tinyspectra.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
-22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			tinyspectra.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
-23	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			tinyspectra.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
-24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
-25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			tinyspectra.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
-26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			tinyspectra.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
-27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			tinyspectra.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
-28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
-29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
-30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
-31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			tinyspectra.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
-32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			tinyspectra.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
-33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
-34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
-35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
-36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
-37	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			tinyspectra.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
-38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			tinyspectra.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
-39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
-40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			tinyspectra.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
-41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			tinyspectra.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
+2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
+3	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
+4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
+5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
+6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
+7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
+8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
+9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
+10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
+11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
+12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
+13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
+14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
+15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
+16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
+17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
+18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
+19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
+21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
+22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
+23	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
+24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
+25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
+26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
+27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
+28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
+29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
+30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
+31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
+32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
+33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
+35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
+36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
+37	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
+38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
+39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
+40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
+41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
+42	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_psm_result2.tabular
--- a/test-data/peptide_shaker_psm_result2.tabular	Sun May 31 09:05:57 2015 -0400
+++ b/test-data/peptide_shaker_psm_result2.tabular	Tue Jun 16 23:43:39 2015 -0400
@@ -1,42 +1,43 @@
 	Protein(s)	Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	Spectrum Scan Number	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	probabilistic PTM score	D-score	Confidence	Validation
-1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			tinyspectra.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
-2	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			tinyspectra.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
-3	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
-4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			tinyspectra.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
-5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			tinyspectra.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
-6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			tinyspectra.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
-7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
-8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			tinyspectra.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
-9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
-10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
-11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
-12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			tinyspectra.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
-13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
-14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
-15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			tinyspectra.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
-16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
-17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			tinyspectra.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
-18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
-19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
-20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			tinyspectra.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
-21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			tinyspectra.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
-22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			tinyspectra.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
-23	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			tinyspectra.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
-24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
-25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			tinyspectra.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
-26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			tinyspectra.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
-27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			tinyspectra.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
-28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
-29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
-30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
-31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			tinyspectra.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
-32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			tinyspectra.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
-33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			tinyspectra.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
-34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			tinyspectra.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
-35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			tinyspectra.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
-36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			tinyspectra.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
-37	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			tinyspectra.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
-38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			tinyspectra.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
-39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			tinyspectra.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
-40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			tinyspectra.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
-41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			tinyspectra.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+1	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 204,  MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
+2	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 591,  MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
+3	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	Cmpd 748,  MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
+4	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 588,  MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
+5	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	Cmpd 81,  MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
+6	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	Cmpd 220,  MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
+7	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 75,  MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
+8	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	Cmpd 752,  MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
+9	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 871,  MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
+10	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	Cmpd 758,  MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
+11	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	Cmpd 39,  MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
+12	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1198,  MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
+13	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 207,  MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
+14	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 875,  MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
+15	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 72,  MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
+16	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	Cmpd 582,  MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
+17	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	Cmpd 736,  MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
+18	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1197,  MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
+19	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	Cmpd 357,  MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+20	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	Cmpd 67,  MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
+21	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	Cmpd 636,  MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
+22	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	INEDRIDELQDKVNK			searchgui_tinyspectra1.mgf	Cmpd 81, +MSn(610.3171), 27.0 min		-1.0	610.31708	3+	3+	1827.9326546837003	0	-1.7717994436305495	0				100.0	Doubtful
+23	cds.comp52727_c0_seq1|m.18670 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 34.52 EValue:1.0e-91, cds.comp52727_c0_seq2|m.18672 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 35.0 EValue:3.0e-92	EIRDEYDNQLNLLSADLESK			searchgui_tinyspectra1.mgf	Cmpd 748, +MSn(789.0604), 76.1 min		-1.0	789.06034	3+	3+	2364.1444886837	0	6.210765906697086	0				100.0	Doubtful
+24	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 204, +MSn(524.2825), 35.5 min		-1.0	524.28252	3+	3+	1569.8362346836998	0	-6.678342042310128	0				100.0	Doubtful
+25	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	YESQLSQIR			searchgui_tinyspectra1.mgf	Cmpd 67, +MSn(562.2947), 26.3 min		-1.0	562.29468	2+	2+	1122.5669286837	0	7.00561302556395	0				100.0	Doubtful
+26	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 72, +MSn(428.2391), 26.6 min		-1.0	428.23909	3+	3+	1281.6928656837001	0	2.0042705774391996	0				100.0	Doubtful
+27	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SLQAENEQLR			searchgui_tinyspectra1.mgf	Cmpd 39, +MSn(594.3056), 25.0 min		-1.0	594.30561	2+	2+	1186.5942146837	0	2.0632379154490605	0				100.0	Doubtful
+28	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 875, +MSn(483.2538), 89.2 min		-1.0	483.25374	3+	3+	1446.7354586837	0	2.7121200881231644	0				100.0	Doubtful
+29	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	VGNLEEELEFLR			searchgui_tinyspectra1.mgf	Cmpd 871, +MSn(724.3762), 88.9 min		-1.0	724.37624	2+	2+	1446.7354586837	0	1.7038016610019715	0				100.0	Doubtful
+30	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	MEIITITNQLQR			searchgui_tinyspectra1.mgf	Cmpd 636, +MSn(730.3981), 66.9 min		-1.0	730.39814	2+	2+	1458.7864506836997	0	-3.233580283650776	0				100.0	Doubtful
+31	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	NLLLDANKENGELK			searchgui_tinyspectra1.mgf	Cmpd 207, +MSn(785.9179), 35.7 min		-1.0	785.91791	2+	2+	1569.8362346836998	0	-9.522288910374096	0				100.0	Doubtful
+32	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 591, +MSn(509.9328), 63.7 min		-1.0	509.93283	3+	3+	1526.7728996836997	0	2.458444778796749	0				100.0	Doubtful
+33	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ASLGMAAGVAGGIATK			searchgui_tinyspectra1.mgf	Cmpd 357, +MSn(687.8723), 46.6 min		-1.0	687.87224	2+	2+	1373.7336876837	0	-2.733506911277659	0				100.0	Doubtful
+34	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1197, +MSn(759.6966), 115.6 min		-1.0	759.69661	3+	3+	2276.0560846836997	0	5.228393373659577	0				100.0	Doubtful
+35	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	LHVEMESMIEELQMLMDAK			searchgui_tinyspectra1.mgf	Cmpd 1198, +MSn(1139.0413), 115.6 min		-1.0	1139.04127	2+	2+	2276.0560846836997	0	5.224764535153943	0				100.0	Doubtful
+36	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISITTYEEEIEDLHATAR			searchgui_tinyspectra1.mgf	Cmpd 752, +MSn(697.6842), 76.3 min		-1.0	697.68418	3+	3+	2090.0167716836995	0	6.659655420038472	0				100.0	Doubtful
+37	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	LISATSISPEHK			searchgui_tinyspectra1.mgf	Cmpd 75, +MSn(641.8547), 26.7 min		-1.0	641.85466	2+	2+	1281.6928656837001	0	1.4811651380377848	0				100.0	Doubtful
+38	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	SHVVGAGLGGGSMGSMNQSMSLHGGR			searchgui_tinyspectra1.mgf	Cmpd 220, +MSn(824.3852), 36.3 min		-1.0	824.38516	3+	3+	2470.1263816837	0	2.9391347559636922	0				100.0	Doubtful
+39	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	KGDIIATVDEWGPVNR			searchgui_tinyspectra1.mgf	Cmpd 582, +MSn(590.6452), 63.2 min		-1.0	590.64518	3+	3+	1768.9107986836998	0	1.6433558579610066	0				100.0	Doubtful
+40	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	ISTGYITENIGGFR			searchgui_tinyspectra1.mgf	Cmpd 588, +MSn(764.3961), 63.5 min		-1.0	764.39611	2+	2+	1526.7728996836997	0	3.1184077735785474	0				100.0	Doubtful
+41	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67	EFDVEPLKEAYQAEIDEAK			searchgui_tinyspectra1.mgf	Cmpd 736, +MSn(742.0258), 75.1 min		-1.0	742.02585	3+	3+	2223.0583016837	0	-1.1594749443833878	0				100.0	Doubtful
+42	cds.comp41779_c0_seq1|m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67, cds.comp41779_c0_seq2|m.9432 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.75 EValue:3.0e-67, cds.comp41779_c0_seq3|m.9435 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 31.94 EValue:4.0e-10	SVISIGEVESEGQYVTLENTSSGR			searchgui_tinyspectra1.mgf	Cmpd 758, +MSn(847.7508), 76.8 min		-1.0	847.75082	3+	3+	2540.2241966836996	0	2.5298047449054923	0				100.0	Doubtful
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_result1.cps
Binary file test-data/peptide_shaker_result1.cps has changed
diff -r 2cafc729b2ae -r dfaea053e32f test-data/peptide_shaker_result1.zip
Binary file test-data/peptide_shaker_result1.zip has changed
diff -r 2cafc729b2ae -r dfaea053e32f test-data/tiny_searchgui_result1.zip
Binary file test-data/tiny_searchgui_result1.zip has changed
diff -r 2cafc729b2ae -r dfaea053e32f test-data/tiny_searchgui_result_amandaonly.zip
Binary file test-data/tiny_searchgui_result_amandaonly.zip has changed
diff -r 2cafc729b2ae -r dfaea053e32f tool_dependencies.xml
--- a/tool_dependencies.xml	Sun May 31 09:05:57 2015 -0400
+++ b/tool_dependencies.xml	Tue Jun 16 23:43:39 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="searchgui" version="1.27">
-        <repository changeset_revision="6ad0463c0e64" name="package_searchgui_1_27" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="searchgui" version="1.28">
+        <repository changeset_revision="0d8bbd52ae42" name="package_searchgui_1_28" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="peptide_shaker" version="0.38">
-        <repository changeset_revision="958037b48c33" name="package_peptideshaker_0_38" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="peptide_shaker" version="0.40">
+        <repository changeset_revision="9a4d33da1cce" name="package_peptideshaker_0_40" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>