--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/201208-378803-cm.pep.xml	Fri Oct 06 15:00:29 2017 -0400
@@ -0,0 +1,10303 @@
+<?xml version="1.0" encoding="UTF-8"?>
+ <msms_pipeline_analysis date="2014-09-19T11:13:55" 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" summary_xml="C:\idpicker\branches\IDPicker-3\TestData\201208-378803.pep.xml">
+ <msms_run_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" msManufacturer="unknown" msModel="unknown" raw_data_type="raw" raw_data=".mzML">
+ <sample_enzyme name="Trypsin/P">
+  <specificity cut="KR" no_cut="-" sense="C"/>
+ </sample_enzyme>
+ <search_summary base_name="C:\idpicker\branches\IDPicker-3\TestData\201208-378803" search_engine="Comet" search_engine_version="2014.02 rev. 0" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1">
+  <search_database local_path="cow.protein.PRG2012-subset.fasta" type="AA"/>
+  <enzymatic_search_constraint enzyme="Trypsin/P" max_num_internal_cleavages="2" min_number_termini="1"/>
+  <aminoacid_modification aminoacid="M" massdiff="15.994900" mass="147.035385" variable="Y" symbol="*"/>
+  <aminoacid_modification aminoacid="Q" massdiff="-17.026000" mass="111.032578" variable="Y" symbol="#"/>
+  <aminoacid_modification aminoacid="Q" massdiff="0.984016" mass="129.042594" variable="Y" symbol="@"/>
+  <aminoacid_modification aminoacid="N" massdiff="0.984016" mass="115.026943" variable="Y" symbol="@"/>
+  <aminoacid_modification aminoacid="C" massdiff="58.005480" mass="161.014665" variable="N"/>
+  <parameter name="# comet_version " value="2014.02"/>
+  <parameter name="activation_method" value="ALL"/>
+  <parameter name="add_A_alanine" value="0.000000"/>
+  <parameter name="add_B_user_amino_acid" value="0.000000"/>
+  <parameter name="add_C_cysteine" value="58.005480"/>
+  <parameter name="add_Cterm_peptide" value="0.000000"/>
+  <parameter name="add_Cterm_protein" value="0.000000"/>
+  <parameter name="add_D_aspartic_acid" value="0.000000"/>
+  <parameter name="add_E_glutamic_acid" value="0.000000"/>
+  <parameter name="add_F_phenylalanine" value="0.000000"/>
+  <parameter name="add_G_glycine" value="0.000000"/>
+  <parameter name="add_H_histidine" value="0.000000"/>
+  <parameter name="add_I_isoleucine" value="0.000000"/>
+  <parameter name="add_J_user_amino_acid" value="0.000000"/>
+  <parameter name="add_K_lysine" value="0.000000"/>
+  <parameter name="add_L_leucine" value="0.000000"/>
+  <parameter name="add_M_methionine" value="0.000000"/>
+  <parameter name="add_N_asparagine" value="0.000000"/>
+  <parameter name="add_Nterm_peptide" value="0.000000"/>
+  <parameter name="add_Nterm_protein" value="0.000000"/>
+  <parameter name="add_O_ornithine" value="0.000000"/>
+  <parameter name="add_P_proline" value="0.000000"/>
+  <parameter name="add_Q_glutamine" value="0.000000"/>
+  <parameter name="add_R_arginine" value="0.000000"/>
+  <parameter name="add_S_serine" value="0.000000"/>
+  <parameter name="add_T_threonine" value="0.000000"/>
+  <parameter name="add_U_user_amino_acid" value="0.000000"/>
+  <parameter name="add_V_valine" value="0.000000"/>
+  <parameter name="add_W_tryptophan" value="0.000000"/>
+  <parameter name="add_X_user_amino_acid" value="0.000000"/>
+  <parameter name="add_Y_tyrosine" value="0.000000"/>
+  <parameter name="add_Z_user_amino_acid" value="0.000000"/>
+  <parameter name="allowed_missed_cleavage" value="2"/>
+  <parameter name="clear_mz_range" value="0.000000 0.000000"/>
+  <parameter name="clip_nterm_methionine" value="1"/>
+  <parameter name="database_name" value="cow.protein.PRG2012-subset.fasta"/>
+  <parameter name="decoy_prefix" value="XXX_"/>
+  <parameter name="decoy_search" value="1"/>
+  <parameter name="digest_mass_range" value="600.000000 5000.000000"/>
+  <parameter name="fragment_bin_offset" value="0.020000"/>
+  <parameter name="fragment_bin_tol" value="0.020000"/>
+  <parameter name="isotope_error" value="1"/>
+  <parameter name="mass_type_fragment" value="1"/>
+  <parameter name="mass_type_parent" value="1"/>
+  <parameter name="max_fragment_charge" value="3"/>
+  <parameter name="max_precursor_charge" value="6"/>
+  <parameter name="max_variable_mods_in_peptide" value="5"/>
+  <parameter name="minimum_intensity" value="0"/>
+  <parameter name="minimum_peaks" value="10"/>
+  <parameter name="ms_level" value="2"/>
+  <parameter name="nucleotide_reading_frame" value="0"/>
+  <parameter name="num_enzyme_termini" value="1"/>
+  <parameter name="num_output_lines" value="5"/>
+  <parameter name="num_results" value="50"/>
+  <parameter name="num_threads" value="0"/>
+  <parameter name="output_outfiles" value="0"/>
+  <parameter name="output_pepxmlfile" value="1"/>
+  <parameter name="output_percolatorfile" value="0"/>
+  <parameter name="output_sqtfile" value="0"/>
+  <parameter name="output_sqtstream" value="0"/>
+  <parameter name="output_suffix" value="-cm"/>
+  <parameter name="output_txtfile" value="0"/>
+  <parameter name="override_charge" value="0"/>
+  <parameter name="peptide_mass_tolerance" value="20.000000"/>
+  <parameter name="peptide_mass_units" value="2"/>
+  <parameter name="precursor_charge" value="1 5"/>
+  <parameter name="print_expect_score" value="1"/>
+  <parameter name="remove_precursor_peak" value="0"/>
+  <parameter name="remove_precursor_tolerance" value="1.500000"/>
+  <parameter name="sample_enzyme_number" value="2"/>
+  <parameter name="scan_range" value="0 0"/>
+  <parameter name="search_enzyme_number" value="2"/>
+  <parameter name="show_fragment_ions" value="0"/>
+  <parameter name="skip_researching" value="1"/>
+  <parameter name="spectrum_batch_size" value="0"/>
+  <parameter name="theoretical_fragment_ions" value="0"/>
+  <parameter name="use_A_ions" value="0"/>
+  <parameter name="use_B_ions" value="1"/>
+  <parameter name="use_C_ions" value="0"/>
+  <parameter name="use_NL_ions" value="1"/>
+  <parameter name="use_X_ions" value="0"/>
+  <parameter name="use_Y_ions" value="1"/>
+  <parameter name="use_Z_ions" value="0"/>
+  <parameter name="use_sparse_matrix" value="0"/>
+  <parameter name="variable_mod01" value="15.994900 M 0 3 -1 0"/>
+  <parameter name="variable_mod02" value="-17.026000 Q 0 1 0 0"/>
+  <parameter name="variable_mod03" value="0.984016 QN 0 3 -1 0"/>
+  <parameter name="variable_mod04" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod05" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod06" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod07" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod08" value="0.000000 X 0 3 -1 0"/>
+  <parameter name="variable_mod09" value="0.000000 X 0 3 -1 0"/>
+ </search_summary>
+ <spectrum_query spectrum="201208-378803.00001.00001.3" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1517.212359" assumed_charge="3" index="1" retention_time_sec="614.4">
+  <search_result>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00001.00001.2" spectrumNativeID="sample=1 period=1 cycle=1181 experiment=2" start_scan="1" end_scan="1" precursor_neutral_mass="1011.474906" assumed_charge="2" index="2" retention_time_sec="614.4">
+  <search_result>
+   <search_hit hit_rank="1" peptide="AEPESDLPR" peptide_prev_aa="H" peptide_next_aa="N" protein="XXX_gi|528920173|ref|XP_001788336.2|" num_tot_proteins="2" num_matched_ions="0" tot_num_ions="16" calc_neutral_pep_mass="1012.482539" massdiff="-1.007633" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
+    <search_score name="xcorr" value="0.474"/>
+    <search_score name="deltacn" value="0.001"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="7"/>
+    <search_score name="expect" value="9.70E+000"/>
+   </search_hit>
+   <search_hit hit_rank="2" peptide="ASQGMTPFR" peptide_prev_aa="G" peptide_next_aa="S" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="16" calc_neutral_pep_mass="1009.465100" massdiff="2.009806" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
+    <modification_info modified_peptide="ASQGM[147]TPFR">
+     <mod_aminoacid_mass position="5" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.473"/>
+    <search_score name="deltacn" value="0.043"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="7"/>
+    <search_score name="expect" value="9.74E+000"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="NESLDLYR" peptide_prev_aa="L" peptide_next_aa="L" protein="XXX_gi|528921178|ref|XP_592304.7|" num_tot_proteins="2" num_matched_ions="1" tot_num_ions="14" calc_neutral_pep_mass="1009.471640" massdiff="2.003266" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
+    <modification_info modified_peptide="N[115]ESLDLYR">
+     <mod_aminoacid_mass position="1" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.453"/>
+    <search_score name="deltacn" value="0.208"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="2.8"/>
+    <search_score name="sprank" value="3"/>
+    <search_score name="expect" value="1.20E+001"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="LMQQSSVSK" peptide_prev_aa="I" peptide_next_aa="F" protein="XXX_gi|30466252|ref|NP_848667.1|" num_tot_proteins="1" num_matched_ions="1" tot_num_ions="16" calc_neutral_pep_mass="1008.479763" massdiff="2.995144" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="622">
+    <modification_info modified_peptide="LMQ[129]Q[129]SSVSK">
+     <mod_aminoacid_mass position="3" mass="129.042594"/>
+     <mod_aminoacid_mass position="4" mass="129.042594"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.359"/>
+    <search_score name="deltacn" value="0.019"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="3.9"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="3.16E+001"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="KAMGSNMEK" peptide_prev_aa="K" peptide_next_aa="Q" protein="XXX_gi|358414198|ref|XP_002700672.2|" num_tot_proteins="4" num_matched_ions="0" tot_num_ions="16" calc_neutral_pep_mass="1010.452487" massdiff="1.022420" num_tol_term="2" num_missed_cleavages="1" num_matched_peptides="622">
+    <modification_info modified_peptide="KAM[147]GSNMEK">
+     <mod_aminoacid_mass position="3" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.352"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="7"/>
+    <search_score name="expect" value="3.39E+001"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00002.00002.2" spectrumNativeID="sample=1 period=1 cycle=1183 experiment=2" start_scan="2" end_scan="2" precursor_neutral_mass="830.315297" assumed_charge="2" index="3" retention_time_sec="617.5">
+  <search_result>
+   <search_hit hit_rank="1" peptide="DGCHWR" peptide_prev_aa="P" peptide_next_aa="G" protein="XXX_gi|528961840|ref|XP_005211303.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="830.312972" massdiff="0.002325" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
+    <modification_info modified_peptide="DGCHWR">
+     <mod_aminoacid_mass position="3" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.208"/>
+    <search_score name="deltacn" value="0.166"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="1.20E+001"/>
+   </search_hit>
+   <search_hit hit_rank="2" peptide="YYNEDQ" peptide_prev_aa="R" peptide_next_aa="L" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="830.308263" massdiff="0.007034" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
+    <search_score name="xcorr" value="0.173"/>
+    <search_score name="deltacn" value="0.133"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="2.36E+001"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="TMEEMR" peptide_prev_aa="F" peptide_next_aa="K" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="827.315310" massdiff="2.999987" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
+    <modification_info modified_peptide="TM[147]EEM[147]R">
+     <mod_aminoacid_mass position="2" mass="147.035385"/>
+     <mod_aminoacid_mass position="5" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.150"/>
+    <search_score name="deltacn" value="0.081"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="3.72E+001"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="WHCGDR" peptide_prev_aa="P" peptide_next_aa="G" protein="gi|528961840|ref|XP_005211303.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="830.312972" massdiff="0.002325" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
+    <modification_info modified_peptide="WHCGDR">
+     <mod_aminoacid_mass position="3" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.138"/>
+    <search_score name="deltacn" value="0.035"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="4.73E+001"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="MEEMTR" peptide_prev_aa="F" peptide_next_aa="K" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="10" calc_neutral_pep_mass="827.315310" massdiff="2.999987" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="76">
+    <modification_info modified_peptide="M[147]EEM[147]TR">
+     <mod_aminoacid_mass position="1" mass="147.035385"/>
+     <mod_aminoacid_mass position="4" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.133"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.0"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="5.20E+001"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00002.00002.3" spectrumNativeID="sample=1 period=1 cycle=1183 experiment=2" start_scan="2" end_scan="2" precursor_neutral_mass="1245.472945" assumed_charge="3" index="4" retention_time_sec="617.5">
+  <search_result>
+   <search_hit hit_rank="1" peptide="VNSGCMAMENK" peptide_prev_aa="R" peptide_next_aa="L" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="1" tot_num_ions="40" calc_neutral_pep_mass="1242.456662" massdiff="3.016283" num_tol_term="2" num_missed_cleavages="0" num_matched_peptides="54">
+    <modification_info modified_peptide="VN[115]SGCMAMEN[115]K">
+     <mod_aminoacid_mass position="2" mass="115.026943"/>
+     <mod_aminoacid_mass position="5" mass="161.014665"/>
+     <mod_aminoacid_mass position="10" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.288"/>
+    <search_score name="deltacn" value="0.321"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.4"/>
+    <search_score name="sprank" value="6"/>
+    <search_score name="expect" value="5.57E+000"/>
+   </search_hit>
+   <search_hit hit_rank="2" peptide="MMTDKEADGSE" peptide_prev_aa="R" peptide_next_aa="T" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" num_matched_ions="2" tot_num_ions="40" calc_neutral_pep_mass="1244.453654" massdiff="1.019291" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="54">
+    <modification_info modified_peptide="M[147]M[147]TDKEADGSE">
+     <mod_aminoacid_mass position="1" mass="147.035385"/>
+     <mod_aminoacid_mass position="2" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.196"/>
+    <search_score name="deltacn" value="0.168"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="3.2"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="2.71E+001"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="MMSASSYNEDL" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|528928354|ref|XP_005193233.1|" num_tot_proteins="1" num_matched_ions="1" tot_num_ions="40" calc_neutral_pep_mass="1246.484589" massdiff="-1.011644" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="54">
+    <search_score name="xcorr" value="0.163"/>
+    <search_score name="deltacn" value="0.284"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.7"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="4.75E+001"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="PYDDDAEYMK" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="3" num_matched_ions="1" tot_num_ions="36" calc_neutral_pep_mass="1245.485970" massdiff="-0.013025" num_tol_term="2" num_missed_cleavages="0" num_matched_peptides="54">
+    <search_score name="xcorr" value="0.117"/>
+    <search_score name="deltacn" value="0.002"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.4"/>
+    <search_score name="sprank" value="5"/>
+    <search_score name="expect" value="1.05E+002"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="CHEVFKQHC" peptide_prev_aa="K" peptide_next_aa="M" protein="XXX_gi|358418103|ref|XP_600387.4|" num_tot_proteins="4" num_matched_ions="1" tot_num_ions="32" calc_neutral_pep_mass="1246.474695" massdiff="-1.001750" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="54">
+    <modification_info modified_peptide="CHEVFKQ[129]HC">
+     <mod_aminoacid_mass position="1" mass="161.014665"/>
+     <mod_aminoacid_mass position="7" mass="129.042594"/>
+     <mod_aminoacid_mass position="9" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.116"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.5"/>
+    <search_score name="sprank" value="4"/>
+    <search_score name="expect" value="1.05E+002"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00003.00003.3" spectrumNativeID="sample=1 period=1 cycle=1186 experiment=2" start_scan="3" end_scan="3" precursor_neutral_mass="1575.554503" assumed_charge="3" index="5" retention_time_sec="621.2">
+  <search_result>
+   <search_hit hit_rank="1" peptide="SSSSASQSNHSCTSM" peptide_prev_aa="R" peptide_next_aa="P" protein="gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="0" tot_num_ions="56" calc_neutral_pep_mass="1574.546067" massdiff="1.008437" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="100">
+    <modification_info modified_peptide="SSSSASQ[129]SNHSCTSM[147]">
+     <mod_aminoacid_mass position="7" mass="129.042594"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+     <mod_aminoacid_mass position="15" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.197"/>
+    <search_score name="deltacn" value="0.185"/>
+    <search_score name="deltacnstar" value="0.003"/>
+    <search_score name="spscore" value="0.0"/>
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+   <search_hit hit_rank="3" peptide="IQVREMDVLDPQ" peptide_prev_aa="R" peptide_next_aa="S" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="44" calc_neutral_pep_mass="1457.718415" massdiff="0.981368" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="1316">
+    <modification_info modified_peptide="IQVREM[147]DVLDPQ">
+     <mod_aminoacid_mass position="6" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.712"/>
+    <search_score name="deltacn" value="0.101"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="10.6"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="1.80E+001"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="NKRDFVSFYQR" peptide_prev_aa="R" peptide_next_aa="R" protein="XXX_gi|529012038|ref|XP_005226889.1|" num_tot_proteins="2" num_matched_ions="4" tot_num_ions="40" calc_neutral_pep_mass="1459.720813" massdiff="-1.021030" num_tol_term="2" num_missed_cleavages="2" num_matched_peptides="1316">
+    <modification_info modified_peptide="N[115]KRDFVSFYQR">
+     <mod_aminoacid_mass position="1" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.640"/>
+    <search_score name="deltacn" value="0.001"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="12.6"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="2.97E+001"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="ELNERNSQIQVQ" peptide_prev_aa="R" peptide_next_aa="A" protein="XXX_gi|528944676|ref|XP_005204734.1|" num_tot_proteins="3" num_matched_ions="2" tot_num_ions="44" calc_neutral_pep_mass="1458.695052" massdiff="0.004731" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="1316">
+    <modification_info modified_peptide="ELN[115]ERNSQIQ[129]VQ">
+     <mod_aminoacid_mass position="3" mass="115.026943"/>
+     <mod_aminoacid_mass position="10" mass="129.042594"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.640"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="2.7"/>
+    <search_score name="sprank" value="12"/>
+    <search_score name="expect" value="2.98E+001"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00108.00108.3" spectrumNativeID="sample=1 period=1 cycle=1627 experiment=2" start_scan="108" end_scan="108" precursor_neutral_mass="1743.773361" assumed_charge="3" index="215" retention_time_sec="1070.9">
+  <search_result>
+   <search_hit hit_rank="1" peptide="MGPTQGGYFPENVKAM" peptide_prev_aa="-" peptide_next_aa="T" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="2" num_matched_ions="1" tot_num_ions="60" calc_neutral_pep_mass="1742.764379" massdiff="1.008982" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="882">
+    <modification_info modified_peptide="MGPTQ[129]GGYFPENVKAM[147]">
+     <mod_aminoacid_mass position="5" mass="129.042594"/>
+     <mod_aminoacid_mass position="16" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.557"/>
+    <search_score name="deltacn" value="0.165"/>
+    <search_score name="deltacnstar" value="0.141"/>
+    <search_score name="spscore" value="0.6"/>
+    <search_score name="sprank" value="7"/>
+    <search_score name="expect" value="4.67E+000"/>
+   </search_hit>
+   <search_hit hit_rank="2" peptide="MGPTQGGYFPENVKAM" peptide_prev_aa="-" peptide_next_aa="T" protein="gi|528921178|ref|XP_592304.7|" num_tot_proteins="2" num_matched_ions="1" tot_num_ions="60" calc_neutral_pep_mass="1741.780363" massdiff="1.992998" num_tol_term="1" num_missed_cleavages="1" num_matched_peptides="882">
+    <modification_info modified_peptide="MGPTQGGYFPENVKAM[147]">
+     <mod_aminoacid_mass position="16" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.479"/>
+    <search_score name="deltacn" value="0.028"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="0.6"/>
+    <search_score name="sprank" value="7"/>
+    <search_score name="expect" value="1.02E+001"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="TTSECLTVTNSSWEK" peptide_prev_aa="V" peptide_next_aa="K" protein="gi|528928354|ref|XP_005193233.1|" num_tot_proteins="1" num_matched_ions="2" tot_num_ions="56" calc_neutral_pep_mass="1743.750912" massdiff="0.022449" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="882">
+    <modification_info modified_peptide="TTSECLTVTN[115]SSWEK">
+     <mod_aminoacid_mass position="5" mass="161.014665"/>
+     <mod_aminoacid_mass position="10" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.465"/>
+    <search_score name="deltacn" value="0.148"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="2.5"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="1.17E+001"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="VLDSKQCFNRGCEK" peptide_prev_aa="P" peptide_next_aa="H" protein="XXX_gi|528908812|ref|XP_609847.5|" num_tot_proteins="12" num_matched_ions="1" tot_num_ions="52" calc_neutral_pep_mass="1743.744388" massdiff="0.028973" num_tol_term="1" num_missed_cleavages="2" num_matched_peptides="882">
+    <modification_info modified_peptide="VLDSKQ[129]CFN[115]RGCEK">
+     <mod_aminoacid_mass position="6" mass="129.042594"/>
+     <mod_aminoacid_mass position="7" mass="161.014665"/>
+     <mod_aminoacid_mass position="9" mass="115.026943"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.396"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="1.3"/>
+    <search_score name="sprank" value="5"/>
+    <search_score name="expect" value="2.32E+001"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="VLDSKQCFNRGCEK" peptide_prev_aa="P" peptide_next_aa="H" protein="XXX_gi|528908812|ref|XP_609847.5|" num_tot_proteins="12" num_matched_ions="1" tot_num_ions="52" calc_neutral_pep_mass="1742.760372" massdiff="1.012989" num_tol_term="1" num_missed_cleavages="2" num_matched_peptides="882">
+    <modification_info modified_peptide="VLDSKQ[129]CFNRGCEK">
+     <mod_aminoacid_mass position="6" mass="129.042594"/>
+     <mod_aminoacid_mass position="7" mass="161.014665"/>
+     <mod_aminoacid_mass position="12" mass="161.014665"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.396"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="1.3"/>
+    <search_score name="sprank" value="5"/>
+    <search_score name="expect" value="2.32E+001"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ <spectrum_query spectrum="201208-378803.00108.00108.2" spectrumNativeID="sample=1 period=1 cycle=1627 experiment=2" start_scan="108" end_scan="108" precursor_neutral_mass="1162.515574" assumed_charge="2" index="216" retention_time_sec="1070.9">
+  <search_result>
+   <search_hit hit_rank="1" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="20" calc_neutral_pep_mass="1163.512853" massdiff="-0.997279" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <modification_info modified_peptide="ISDMN[115]QNIGAT">
+     <mod_aminoacid_mass position="5" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.721"/>
+    <search_score name="deltacn" value="0.290"/>
+    <search_score name="deltacnstar" value="0.063"/>
+    <search_score name="spscore" value="28.2"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="1.00E+000"/>
+   </search_hit>
+   <search_hit hit_rank="2" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="20" calc_neutral_pep_mass="1163.512853" massdiff="-0.997279" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <modification_info modified_peptide="ISDMNQ[129]NIGAT">
+     <mod_aminoacid_mass position="6" mass="129.042594"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.675"/>
+    <search_score name="deltacn" value="0.242"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="28.2"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="1.00E+000"/>
+   </search_hit>
+   <search_hit hit_rank="3" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="4" tot_num_ions="20" calc_neutral_pep_mass="1163.512853" massdiff="-0.997279" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <modification_info modified_peptide="ISDMNQN[115]IGAT">
+     <mod_aminoacid_mass position="7" mass="115.026943"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.675"/>
+    <search_score name="deltacn" value="0.242"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="28.2"/>
+    <search_score name="sprank" value="1"/>
+    <search_score name="expect" value="1.00E+000"/>
+   </search_hit>
+   <search_hit hit_rank="4" peptide="VIDEGLMDEK" peptide_prev_aa="E" peptide_next_aa="L" protein="gi|528944676|ref|XP_005204734.1|" num_tot_proteins="1" num_matched_ions="1" tot_num_ions="18" calc_neutral_pep_mass="1163.537991" massdiff="-1.022417" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <modification_info modified_peptide="VIDEGLM[147]DEK">
+     <mod_aminoacid_mass position="7" mass="147.035385"/>
+    </modification_info>
+    <search_score name="xcorr" value="0.512"/>
+    <search_score name="deltacn" value="0.077"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="3.7"/>
+    <search_score name="sprank" value="3"/>
+    <search_score name="expect" value="2.60E+000"/>
+   </search_hit>
+   <search_hit hit_rank="5" peptide="ISDMNQNIGAT" peptide_prev_aa="K" peptide_next_aa="E" protein="XXX_gi|528944678|ref|XP_005204735.1|" num_tot_proteins="3" num_matched_ions="3" tot_num_ions="20" calc_neutral_pep_mass="1162.528837" massdiff="-0.013263" num_tol_term="1" num_missed_cleavages="0" num_matched_peptides="562">
+    <search_score name="xcorr" value="0.473"/>
+    <search_score name="deltacn" value="1.000"/>
+    <search_score name="deltacnstar" value="0.000"/>
+    <search_score name="spscore" value="15.4"/>
+    <search_score name="sprank" value="2"/>
+    <search_score name="expect" value="4.02E+000"/>
+   </search_hit>
+  </search_result>
+ </spectrum_query>
+ </msms_run_summary>
+</msms_pipeline_analysis>