Mercurial > repos > iracooke > tpp_prophets
changeset 14:d90c8bc10a9c draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 19:55:19 -0400 |
| parents | b793fe628648 |
| children | 0746a2ae9e04 |
| files | README.md README.rst interprophet.xml peptide_prophet.xml pepxml_to_table.xml protein_prophet.xml protxml_to_table.xml repository_dependencies.xml test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml |
| diffstat | 10 files changed, 2037 insertions(+), 45 deletions(-) [+] |
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--- a/README.md Tue Jul 01 11:16:41 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -## What is it? -Galaxy tool definition files and wrapper scripts for Peptide and Protein inference tools in the [Trans Proteomic Pipeline](http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP) (Peptide Prophet, iProphet and Protein Prophet). - -## Installation -Install from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ - -All the tools depend on command-line scripts and databases available in the [protk ruby gem](https://bitbucket.org/iracooke/protk). -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Mar 26 19:55:19 2015 -0400 @@ -0,0 +1,37 @@ +TPP Prophets +============ + +Galaxy wrappers for Peptide Prophet, iProphet and Protein Prophet + +Requirements +------------ + +This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_ + +Please visit the TPP__ website for details of the various Prophet tools + +__ trans_proteomic_pipeline_
--- a/interprophet.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/interprophet.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,8 +1,9 @@ -<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1"> +<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.0"> <requirements> - <requirement type="package" version="1.3">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> </requirements> @@ -22,35 +23,34 @@ $use_nsm - --minprob $minprob + --p-thresh $p_thresh + + --threads $threads - ## Inputs. - ${first_input} - #for $input_file in $input_files: - ${input_file.additional_input} - #end for +#for $pepxml_file in $pepxml_files: + ${pepxml_file} +#end for </command> + <inputs> - <param name="first_input" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> - - <repeat name="input_files" title="Additional PepXML Input Files"> - <param format="peptideprophet_pepxml" name="additional_input" type="data" label="PepXML produced by Peptide Prophet" help=""/> - </repeat> + <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + + <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/> + <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/> + <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/> + <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/> + <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/> - <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="blank" falsevalue="--no-nss"/> - <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="blank" falsevalue="--no-nrs"/> - <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="blank" falsevalue="--no-nse"/> - <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="blank" falsevalue="--no-nsi"/> - <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="blank" falsevalue="--no-nsm"/> - - <param name="minprob" type="text" label="Minimum threshod probability for reporting results"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + + <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> </inputs> <outputs> - <data format="interprophet_pepxml" name="output" metadata_source="first_input" label="interprophet.${first_input.display_name}" from_work_dir="interprophet_output.pep.xml"/> + <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/> </outputs> <help>
--- a/peptide_prophet.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/peptide_prophet.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,7 +1,8 @@ -<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1"> +<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.0"> <requirements> - <requirement type="package" version="1.3">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> </requirements> <description>Calculate Peptide Prophet statistics on search results</description> @@ -23,6 +24,16 @@ $force_fit $allow_alt_instruments $maldi + $usedecoys + --decoy-prefix $decoy_prefix_string + +#if $experiment_label + --experiment-label $experiment_label +#end if + + --p-thresh $p_thresh + + --threads $threads </command> @@ -44,18 +55,23 @@ <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> - + <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> + <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> + <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> </inputs> <outputs> <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> </outputs> + <help> **What it does** -Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments. From a practical perspective it estimates the probability that each peptide assignment is correct (providing probabilities as outputs), given raw scores (possibly on some arbitrary scale) as inputs. +Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments. ----
--- a/pepxml_to_table.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/pepxml_to_table.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,7 +1,8 @@ -<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.1"> +<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.0"> <requirements> - <requirement type="package" version="1.3">protk</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> </requirements> @@ -10,18 +11,33 @@ <!-- Note .. the input file is assumed to be the first argument --> -<command>pepxml_to_table.rb $input_file -o $output</command> +<command>pepxml_to_table.rb $input_file -o $output $invert_probs</command> <inputs> <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> + <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> </inputs> <outputs> <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> </outputs> + + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/> + <output name="output" format="csv"> + <assert_contents> + <has_text text="ANTNNYAPKSSR" /> + </assert_contents> + </output> + </test> + </tests> + + <help> Convert a pepXML file to Tab delimited text </help>
--- a/protein_prophet.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/protein_prophet.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,7 +1,8 @@ -<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1"> +<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.0"> <requirements> - <requirement type="package" version="1.3">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> </requirements> <description>Calculate Protein Prophet statistics on search results</description> @@ -35,7 +36,6 @@ <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> - <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/>
--- a/protxml_to_table.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/protxml_to_table.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,12 +1,14 @@ -<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.0.1"> +<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.0"> <requirements> - <requirement type="package" version="1.3">protk</requirement> + <container type="docker">iracooke/protk-1.4.1</container> + <requirement type="package" version="1.4">protk</requirement> </requirements> <description>Converts a ProtXML file to a table</description> <command> protxml_to_table.rb + $invert_probs $input_file -o $output @@ -15,7 +17,7 @@ <inputs> <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> - + <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> </inputs> @@ -23,6 +25,18 @@ <data format="tabular" name="output" /> </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/> + <output name="output" format="tabular"> + <assert_contents> + <has_text text="AVQKYLTAHEQSK" /> + </assert_contents> + </output> + </test> + </tests> + <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Mar 26 19:55:19 2015 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="Proteomics datatypes"> + <repository changeset_revision="ac51d9dbfb4d" name="proteomics_datatypes" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml Thu Mar 26 19:55:19 2015 -0400 @@ -0,0 +1,1651 @@ +<?xml version="1.0" encoding="UTF-8"?> +<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?> +<msms_pipeline_analysis date="2014-06-22T13:57:05" summary_xml="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"> + <msms_run_summary base_name="mr176-BSA100fmole_BA3_01_8168.d_tandem" search_engine="X! Tandem" raw_data_type="raw" raw_data=".?"> + <sample_enzyme name="trypsin"> +<specificity cut="KR" no_cut="P" sense="C"/> +</sample_enzyme> +<search_summary base_name="mr176-BSA100fmole_BA3_01_8168.d_tandem" search_engine="X! Tandem" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1"> + <search_database local_path="/Users/icooke/Desktop/iptest/AASequences.fasta" type="AA"/> + <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="1" /> + <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> + <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0354" variable="Y" /> + <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> + <terminal_modification terminus="n" massdiff="42.0106" mass="43.0184" protein_terminus="N" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> + + <!-- Input parameters --> + <parameter name="list path, default parameters" value="/Users/icooke/.rvm/gems/ruby-2.0.0-p353/gems/protk-1.2.6.pre6/lib/protk/data/tandem_isb_native_defaults.xml"/> + <parameter name="list path, taxonomy information" value="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem.taxonomy.xml"/> + <parameter name="output, histogram column width" value="30"/> + <parameter name="output, histograms" value="no"/> + <parameter name="output, log path" value=""/> + <parameter name="output, maximum valid expectation value" value="0.1"/> + <parameter name="output, message" value="1234567890"/> + <parameter name="output, one sequence copy" value="no"/> + <parameter name="output, parameters" value="yes"/> + <parameter name="output, path" value="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem"/> + <parameter name="output, path hashing" value="no"/> + <parameter name="output, performance" value="yes"/> + <parameter name="output, proteins" value="yes"/> + <parameter name="output, results" value="all"/> + <parameter name="output, sequence path" value=""/> + <parameter name="output, sequences" value="no"/> + <parameter name="output, sort results by" value="spectrum"/> + <parameter name="output, spectra" value="no"/> + <parameter name="output, xsl path" value="tandem-style.xsl"/> + <parameter name="protein, C-terminal residue modification mass" value=""/> + <parameter name="protein, N-terminal residue modification mass" value=""/> + <parameter name="protein, cleavage C-terminal mass change" value=""/> + <parameter name="protein, cleavage N-terminal mass change" value=""/> + <parameter name="protein, cleavage semi" value="yes"/> + <parameter name="protein, cleavage site" value="[RK]|{P}"/> + <parameter name="protein, homolog management" value="no"/> + <parameter name="protein, modified residue mass file" value=""/> + <parameter name="protein, quick acetyl" value="yes"/> + <parameter name="protein, taxon" value="AASequences.fasta"/> + <parameter name="refine" value="no"/> + <parameter name="refine, maximum valid expectation value" value="0.1"/> + <parameter name="refine, sequence path" value=""/> + <parameter name="refine, spectrum synthesis" value="yes"/> + <parameter name="residue, modification mass" value=""/> + <parameter name="residue, potential modification mass" value="15.994915@M"/> + <parameter name="residue, potential modification motif" value=""/> + <parameter name="scoring, a ions" value="no"/> + <parameter name="scoring, b ions" value="yes"/> + <parameter name="scoring, c ions" value="no"/> + <parameter name="scoring, cyclic permutation" value="no"/> + <parameter name="scoring, include reverse" value="no"/> + <parameter name="scoring, maximum missed cleavage sites" value="2"/> + <parameter name="scoring, minimum ion count" value="4"/> + <parameter name="scoring, x ions" value="no"/> + <parameter name="scoring, y ions" value="yes"/> + <parameter name="scoring, z ions" value="no"/> + <parameter name="spectrum, dynamic range" value="100.0"/> + <parameter name="spectrum, fragment mass type" value="monoisotopic"/> + <parameter name="spectrum, fragment monoisotopic mass error" value="0.4"/> + <parameter name="spectrum, fragment monoisotopic mass error units" value="Daltons"/> + <parameter name="spectrum, maximum parent charge" value="5"/> + <parameter name="spectrum, minimum fragment mz" value="50.0"/> + <parameter name="spectrum, minimum parent m+h" value="600.0"/> + <parameter name="spectrum, minimum peaks" value="6"/> + <parameter name="spectrum, parent monoisotopic mass error minus" value="100.0"/> + <parameter name="spectrum, parent monoisotopic mass error plus" value="100.0"/> + <parameter name="spectrum, parent monoisotopic mass error units" value="Daltons"/> + <parameter name="spectrum, parent monoisotopic mass isotope error" value="no"/> + <parameter name="spectrum, path" value="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d.mgf"/> + <parameter name="spectrum, sequence batch size" value="1000"/> + <parameter name="spectrum, threads" value="1"/> + <parameter name="spectrum, total peaks" value="50"/> + <parameter name="spectrum, use conditioning" value="yes"/> + <parameter name="spectrum, use noise suppression" value="no"/> + <!-- Unused input parameters --> + <parameter name="protein, use minimal annotations" value="yes"/> + <parameter name="refine, modification mass" value=""/> + <parameter name="refine, point mutations" value="no"/> + <parameter name="refine, potential C-terminus modifications" value=""/> + <parameter name="refine, potential N-terminus modifications" value=""/> + <parameter name="refine, potential modification mass" value=""/> + <parameter name="refine, potential modification motif" value=""/> + <parameter name="refine, tic percent" value="10"/> + <parameter name="refine, unanticipated cleavage" value="no"/> + <parameter name="refine, use potential modifications for full refinement" value="no"/> + <parameter name="scoring, pluggable scoring" value="no"/> + <parameter name="spectrum, maximum parent m+h" value="4000.0"/> + <!-- Performance parameters --> + <parameter name="list path, sequence source #1" value="/Users/icooke/Desktop/iptest/AASequences.fasta"/> + <parameter name="list path, sequence source description #1" value="no description"/> + <parameter name="modelling, duplicate peptide ids" value="0"/> + <parameter name="modelling, duplicate proteins" value="0"/> + <parameter name="modelling, total peptides used" value="542390"/> + <parameter name="modelling, total proteins used" value="33"/> + <parameter name="modelling, total spectra used" value="118"/> + <parameter name="process, start time" value="2014:06:22:13:57:05"/> + <parameter name="process, version" value="X! Tandem Sledgehammer (2013.09.01.1)"/> + <parameter name="quality values" value="12 10 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/> + <parameter name="refining, # input models" value="0"/> + <parameter name="refining, # input spectra" value="0"/> + <parameter name="refining, # partial cleavage" value="0"/> + <parameter name="refining, # point mutations" value="0"/> + <parameter name="refining, # potential C-terminii" value="0"/> + <parameter name="refining, # potential N-terminii" value="0"/> + <parameter name="refining, # unanticipated cleavage" value="0"/> + <parameter name="timing, initial modelling total (sec)" value="0.63"/> + <parameter name="timing, initial modelling/spectrum (sec)" value="0.0053"/> + <parameter name="timing, load sequence models (sec)" value="0.00"/> + <parameter name="timing, refinement/spectrum (sec)" value="0.0000"/> + </search_summary> + + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00001.00001.2" start_scan="1" end_scan="1" precursor_neutral_mass="1442.6899" assumed_charge="2" index="1"> + <search_result> + <search_hit hit_rank="1" peptide="DLIRQQCYLFN" peptide_prev_aa="K" peptide_next_aa="H" protein="sp|Q26604|SMOX5_SCHMA" protein_descr="Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="20" calc_neutral_pep_mass="1393.6817" massdiff="49.008" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="19.0"/> + <search_score name="nextscore" value="19.0"/> + <search_score name="bscore" value="3.2"/> + <search_score name="yscore" value="10.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00002.00002.3" start_scan="2" end_scan="2" precursor_neutral_mass="1248.6649" assumed_charge="3" index="2"> + <search_result> + <search_hit hit_rank="1" peptide="ANTNNYAPKSSR" peptide_prev_aa="A" peptide_next_aa="N" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="44" calc_neutral_pep_mass="1303.6267" massdiff="-54.962" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="20.6"/> + <search_score name="nextscore" value="20.6"/> + <search_score name="bscore" value="9.2"/> + <search_score name="yscore" value="10.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query 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protein_name="tr|Q9YH59|Q9YH59_CHICK" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="FMAPSSGMNMGGMGG" group_sibling_id="a" total_number_peptides="0" confidence="0.0611"> + <parameter name="prot_length" value="344"/> + <annotation protein_description="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1"/> + <peptide peptide_sequence="FMAPSSGMNMGGMGG" charge="2" initial_probability="0.0864" nsp_adjusted_probability="0.0833" fpkm_adjusted_probability="0.0833" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.09" is_contributing_evidence="N" calc_neutral_pep_mass="1460.5197"> +<modification_info modified_peptide="FM[147]APSSGMNM[147]GGM[147]GG"> +<mod_aminoacid_mass position="2" mass="147.035400"/> +<mod_aminoacid_mass position="10" mass="147.035400"/> +<mod_aminoacid_mass position="13" mass="147.035400"/> +</modification_info> + </peptide> + </protein> +</protein_group> +</protein_summary>