RubyGems - mspire - Versions diffs - 0.2.4 → 0.3.0 - Mend

mspire 0.2.4 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (233) hide show

data/INSTALL +1 -0
data/README +25 -0
data/Rakefile +129 -40
data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
data/bin/bioworks_to_pepxml.rb +1 -0
data/bin/fasta_shaker.rb +1 -96
data/bin/filter_and_validate.rb +5 -0
data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
data/bin/prob_validate.rb +6 -0
data/bin/raw_to_mzXML.rb +2 -2
data/bin/srf_group.rb +1 -0
data/bin/srf_to_sqt.rb +40 -0
data/changelog.txt +68 -0
data/lib/align/chams.rb +6 -6
data/lib/align.rb +4 -3
data/lib/bsearch.rb +120 -0
data/lib/fasta.rb +318 -86
data/lib/group_by.rb +10 -0
data/lib/index_by.rb +11 -0
data/lib/merge_deep.rb +21 -0
data/lib/{spec → ms/converter}/mzxml.rb +77 -109
data/lib/ms/gradient_program.rb +171 -0
data/lib/ms/msrun.rb +209 -0
data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
data/lib/ms/parser/mzdata/axml.rb +12 -0
data/lib/ms/parser/mzdata/dom.rb +160 -0
data/lib/ms/parser/mzdata/libxml.rb +7 -0
data/lib/ms/parser/mzdata.rb +25 -0
data/lib/ms/parser/mzxml/axml.rb +11 -0
data/lib/ms/parser/mzxml/dom.rb +159 -0
data/lib/ms/parser/mzxml/hpricot.rb +253 -0
data/lib/ms/parser/mzxml/libxml.rb +15 -0
data/lib/ms/parser/mzxml/regexp.rb +122 -0
data/lib/ms/parser/mzxml/rexml.rb +72 -0
data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
data/lib/ms/parser/mzxml.rb +175 -0
data/lib/ms/parser.rb +108 -0
data/lib/ms/precursor.rb +10 -0
data/lib/ms/scan.rb +81 -0
data/lib/ms/spectrum.rb +193 -0
data/lib/ms.rb +10 -0
data/lib/mspire.rb +4 -0
data/lib/roc.rb +61 -1
data/lib/sample_enzyme.rb +31 -8
data/lib/scan_i.rb +21 -0
data/lib/spec_id/aa_freqs.rb +7 -3
data/lib/spec_id/bioworks.rb +20 -14
data/lib/spec_id/digestor.rb +139 -0
data/lib/spec_id/mass.rb +116 -0
data/lib/spec_id/parser/proph.rb +236 -0
data/lib/spec_id/precision/filter/cmdline.rb +209 -0
data/lib/spec_id/precision/filter/interactive.rb +134 -0
data/lib/spec_id/precision/filter/output.rb +147 -0
data/lib/spec_id/precision/filter.rb +623 -0
data/lib/spec_id/precision/output.rb +60 -0
data/lib/spec_id/precision/prob/cmdline.rb +139 -0
data/lib/spec_id/precision/prob/output.rb +88 -0
data/lib/spec_id/precision/prob.rb +171 -0
data/lib/spec_id/proph/pep_summary.rb +92 -0
data/lib/spec_id/proph/prot_summary.rb +484 -0
data/lib/spec_id/proph.rb +2 -466
data/lib/spec_id/protein_summary.rb +2 -2
data/lib/spec_id/sequest/params.rb +316 -0
data/lib/spec_id/sequest/pepxml.rb +1513 -0
data/lib/spec_id/sequest.rb +2 -1672
data/lib/spec_id/srf.rb +445 -177
data/lib/spec_id.rb +183 -95
data/lib/spec_id_xml.rb +8 -10
data/lib/transmem/phobius.rb +147 -0
data/lib/transmem/toppred.rb +368 -0
data/lib/transmem.rb +157 -0
data/lib/validator/aa.rb +135 -0
data/lib/validator/background.rb +73 -0
data/lib/validator/bias.rb +95 -0
data/lib/validator/cmdline.rb +260 -0
data/lib/validator/decoy.rb +94 -0
data/lib/validator/digestion_based.rb +69 -0
data/lib/validator/probability.rb +48 -0
data/lib/validator/prot_from_pep.rb +234 -0
data/lib/validator/transmem.rb +272 -0
data/lib/validator/true_pos.rb +46 -0
data/lib/validator.rb +214 -0
data/lib/xml.rb +38 -0
data/lib/xml_style_parser.rb +105 -0
data/lib/xmlparser_wrapper.rb +19 -0
data/script/compile_and_plot_smriti_final.rb +97 -0
data/script/extract_gradient_programs.rb +56 -0
data/script/get_apex_values_rexml.rb +44 -0
data/script/mzXML2timeIndex.rb +1 -1
data/script/smriti_final_analysis.rb +103 -0
data/script/toppred_to_yaml.rb +47 -0
data/script/tpp_installer.rb +1 -1
data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
data/specs/bin/fasta_shaker_spec.rb +259 -0
data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
data/specs/bin/filter_and_validate_spec.rb +124 -0
data/specs/bin/ms_to_lmat_spec.rb +34 -0
data/specs/bin/prob_validate_spec.rb +62 -0
data/specs/bin/protein_summary_spec.rb +10 -0
data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
data/specs/gi_spec.rb +22 -0
data/specs/load_bin_path.rb +7 -0
data/specs/merge_deep_spec.rb +13 -0
data/specs/ms/gradient_program_spec.rb +77 -0
data/specs/ms/msrun_spec.rb +455 -0
data/specs/ms/parser_spec.rb +92 -0
data/specs/ms/spectrum_spec.rb +89 -0
data/specs/roc_spec.rb +251 -0
data/specs/rspec_autotest.rb +149 -0
data/specs/sample_enzyme_spec.rb +41 -0
data/specs/spec_helper.rb +133 -0
data/specs/spec_id/aa_freqs_spec.rb +52 -0
data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
data/specs/spec_id/digestor_spec.rb +75 -0
data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
data/specs/spec_id/precision/filter/output_spec.rb +31 -0
data/specs/spec_id/precision/filter_spec.rb +243 -0
data/specs/spec_id/precision/prob_spec.rb +111 -0
data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
data/specs/spec_id/sequest/params_spec.rb +68 -0
data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
data/specs/spec_id/sqt_spec.rb +138 -0
data/specs/spec_id/srf_spec.rb +209 -0
data/specs/spec_id/srf_spec_helper.rb +302 -0
data/specs/spec_id_helper.rb +33 -0
data/specs/spec_id_spec.rb +361 -0
data/specs/spec_id_xml_spec.rb +33 -0
data/specs/transmem/phobius_spec.rb +423 -0
data/specs/transmem/toppred_spec.rb +297 -0
data/specs/transmem_spec.rb +60 -0
data/specs/transmem_spec_shared.rb +64 -0
data/specs/validator/aa_spec.rb +107 -0
data/specs/validator/background_spec.rb +51 -0
data/specs/validator/bias_spec.rb +146 -0
data/specs/validator/decoy_spec.rb +51 -0
data/specs/validator/fasta_helper.rb +26 -0
data/specs/validator/prot_from_pep_spec.rb +141 -0
data/specs/validator/transmem_spec.rb +145 -0
data/specs/validator/true_pos_spec.rb +58 -0
data/specs/validator_helper.rb +33 -0
data/specs/xml_spec.rb +12 -0
data/test_files/000_pepxml18_small.xml +206 -0
data/test_files/020a.mzXML.timeIndex +4710 -0
data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
data/test_files/4-03-03_small-prot.xml +321 -0
data/test_files/4-03-03_small.xml +3876 -0
data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
data/test_files/bioworks-3.3_10prots.xml +5999 -0
data/test_files/bioworks31.params +77 -0
data/test_files/bioworks32.params +62 -0
data/test_files/bioworks33.params +63 -0
data/test_files/bioworks_single_run_small.xml +7237 -0
data/test_files/bioworks_small.fasta +212 -0
data/test_files/bioworks_small.params +63 -0
data/test_files/bioworks_small.phobius +109 -0
data/test_files/bioworks_small.toppred.out +2847 -0
data/test_files/bioworks_small.xml +5610 -0
data/test_files/bioworks_with_INV_small.xml +3753 -0
data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
data/test_files/corrupted_900.srf +0 -0
data/test_files/head_of_7MIX.srf +0 -0
data/test_files/interact-opd1_mods_small-prot.xml +304 -0
data/test_files/messups.fasta +297 -0
data/test_files/opd1/000.my_answer.100lines.xml +101 -0
data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
data/test_files/opd1/000_020-prot.png +0 -0
data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
data/test_files/opd1/000_020_3prots-prot.xml +62 -0
data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
data/test_files/opd1/sequest.3.1.params +77 -0
data/test_files/opd1/sequest.3.2.params +62 -0
data/test_files/opd1/twenty_scans.mzXML +418 -0
data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
data/test_files/opd1/twenty_scans_answ.lmat +0 -0
data/test_files/opd1/twenty_scans_answ.lmata +9 -0
data/test_files/opd1_020_beginning.RAW +0 -0
data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
data/test_files/pepproph_small.xml +4691 -0
data/test_files/phobius.small.noheader.txt +50 -0
data/test_files/phobius.small.small.txt +53 -0
data/test_files/s01_anC1_ld020mM.key.txt +25 -0
data/test_files/s01_anC1_ld020mM.meth +0 -0
data/test_files/small.fasta +297 -0
data/test_files/smallraw.RAW +0 -0
data/test_files/tf_bioworks2excel.bioXML +14340 -0
data/test_files/tf_bioworks2excel.txt.actual +1035 -0
data/test_files/toppred.small.out +416 -0
data/test_files/toppred.xml.out +318 -0
data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
data/test_files/yeast_gly_small-prot.xml +265 -0
data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
data/test_files/yeast_gly_small.xml +3807 -0
data/test_files/yeast_gly_small2.parentTimes +6 -0
metadata +273 -57
data/bin/filter.rb +0 -6
data/bin/precision.rb +0 -5
data/lib/spec/mzdata/parser.rb +0 -108
data/lib/spec/mzdata.rb +0 -48
data/lib/spec/mzxml/parser.rb +0 -449
data/lib/spec/scan.rb +0 -55
data/lib/spec_id/filter.rb +0 -797
data/lib/spec_id/precision.rb +0 -421
data/lib/toppred.rb +0 -18
data/script/filter-peps.rb +0 -164
data/test/tc_aa_freqs.rb +0 -59
data/test/tc_fasta_shaker.rb +0 -149
data/test/tc_filter.rb +0 -203
data/test/tc_filter_peps.rb +0 -46
data/test/tc_gi.rb +0 -17
data/test/tc_id_class_anal.rb +0 -70
data/test/tc_id_precision.rb +0 -89
data/test/tc_msrun.rb +0 -88
data/test/tc_mzxml.rb +0 -88
data/test/tc_mzxml_to_lmat.rb +0 -36
data/test/tc_peptide_parent_times.rb +0 -27
data/test/tc_precision.rb +0 -60
data/test/tc_roc.rb +0 -166
data/test/tc_sample_enzyme.rb +0 -32
data/test/tc_scan.rb +0 -26
data/test/tc_sequest.rb +0 -336
data/test/tc_spec.rb +0 -78
data/test/tc_spec_id.rb +0 -201
data/test/tc_spec_id_xml.rb +0 -36
data/test/tc_srf.rb +0 -262

data/test_files/000_pepxml18_small.xml ADDED Viewed

@@ -0,0 +1,206 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="/tools/bin/TPP/tpp/schema/pepXML_std.xsl"?>
+<msms_pipeline_analysis date="2006-07-20T17:23:26" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd" summary_xml="000.xml">
+<msms_run_summary base_name="/work/john/021112.EcoliSol37.1/000" msManufacturer="ThermoFinnigan" msModel="LCQ Classic" msIonization="ESI" msMassAnalyzer="Ion Trap" msDetector="UNKNOWN" raw_data_type="raw" raw_data=".mzXML">
+<sample_enzyme name="trypsin">
+<specificity cut="KR" no_cut="P" sense="C"/>
+</sample_enzyme>
+<search_summary base_name="/work/john/021112.EcoliSol37.1/000" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="average" out_data_type="out" out_data=".tgz" search_id="1">
+<search_database local_path="/work/ms/database/ecoli_K12.fasta" type="AA"/>
+<enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/>
+<parameter name="peptide_mass_tol" value="1.500"/>
+<parameter name="fragment_ion_tol" value="0.000"/>
+<parameter name="ion_series" value=" 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0"/>
+<parameter name="max_num_differential_AA_per_mod" value="4"/>
+<parameter name="nucleotide_reading_frame" value="0"/>
+<parameter name="num_output_lines" value="10"/>
+<parameter name="remove_precursor_peak" value="0"/>
+<parameter name="ion_cutoff_percentage" value="0.0"/>
+<parameter name="match_peak_count" value="0"/>
+<parameter name="match_peak_allowed_error" value="1"/>
+<parameter name="match_peak_tolerance" value="1.0"/>
+<parameter name="protein_mass_filter" value="0 0"/>
+<parameter name="sequence_header_filter" value=""/>
+</search_summary>
+    <spectrum_query spectrum="000.100.100.1" start_scan="100" end_scan="100" precursor_neutral_mass="1074.5920" assumed_charge="1" index="1">
+    <search_result>      <search_hit hit_rank="1" peptide="SIYFRNFK" peptide_prev_aa="R" peptide_next_aa="G" protein="gi|16130084|ref|NP_416651.1|" num_tot_proteins="1" num_matched_ions="  4" tot_num_ions=" 14" calc_neutral_pep_mass="1074.1920" massdiff="+0.4" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
+        <search_score name="xcorr" value="0.400"/>
+        <search_score name="deltacn" value="0.023"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="78.8"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1000.1000.1" start_scan="1000" end_scan="1000" precursor_neutral_mass="663.1920" assumed_charge="1" index="2">
+    <search_result>      <search_hit hit_rank="1" peptide="ALADFK" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|16128765|ref|NP_415318.1|" num_tot_proteins="1" num_matched_ions="  5" tot_num_ions=" 10" calc_neutral_pep_mass="663.7920" massdiff="-0.6" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="0.965"/>
+        <search_score name="deltacn" value="0.132"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="81.1"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1002.1002.1" start_scan="1002" end_scan="1002" precursor_neutral_mass="1291.6920" assumed_charge="1" index="3">
+    <search_result>      <search_hit hit_rank="1" peptide="EETEWRVQSK" peptide_prev_aa="R" peptide_next_aa="R" protein="gi|16128280|ref|NP_414829.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 18" calc_neutral_pep_mass="1291.3920" massdiff="+0.3" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
+        <search_score name="xcorr" value="0.904"/>
+        <search_score name="deltacn" value="0.041"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="140.0"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1003.1003.1" start_scan="1003" end_scan="1003" precursor_neutral_mass="769.3920" assumed_charge="1" index="4">
+    <search_result>      <search_hit hit_rank="1" peptide="NIGLLNK" peptide_prev_aa="R" peptide_next_aa="I" protein="gi|16129238|ref|NP_415793.1|" num_tot_proteins="1" num_matched_ions="  8" tot_num_ions=" 12" calc_neutral_pep_mass="770.8920" massdiff="-1.5" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="0.887"/>
+        <search_score name="deltacn" value="0.115"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="153.1"/>
+        <search_score name="sprank" value="2"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1004.1004.2" start_scan="1004" end_scan="1004" precursor_neutral_mass="1252.2920" assumed_charge="2" index="5">
+    <search_result>      <search_hit hit_rank="1" peptide="QLTYTAHGPHK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131568|ref|NP_418155.1|" num_tot_proteins="1" num_matched_ions="  7" tot_num_ions=" 20" calc_neutral_pep_mass="1252.3920" massdiff="-0.1" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="1.066"/>
+        <search_score name="deltacn" value="0.172"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="125.2"/>
+        <search_score name="sprank" value="10"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1004.1004.3" start_scan="1004" end_scan="1004" precursor_neutral_mass="1878.4920" assumed_charge="3" index="6">
+    <search_result>      <search_hit hit_rank="1" peptide="AGNARVVNSNAMSFLAQK" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|16131337|ref|NP_417922.1|" num_tot_proteins="1" num_matched_ions=" 16" tot_num_ions=" 68" calc_neutral_pep_mass="1878.0920" massdiff="+0.4" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
+        <search_score name="xcorr" value="1.370"/>
+        <search_score name="deltacn" value="0.199"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="245.0"/>
+        <search_score name="sprank" value="2"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1006.1006.2" start_scan="1006" end_scan="1006" precursor_neutral_mass="888.1920" assumed_charge="2" index="7">
+    <search_result>      <search_hit hit_rank="1" peptide="GNSRDIVK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131041|ref|NP_417618.1|" num_tot_proteins="1" num_matched_ions="  9" tot_num_ions=" 14" calc_neutral_pep_mass="887.9920" massdiff="+0.2" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
+        <search_score name="xcorr" value="0.982"/>
+        <search_score name="deltacn" value="0.006"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="267.3"/>
+        <search_score name="sprank" value="6"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1006.1006.3" start_scan="1006" end_scan="1006" precursor_neutral_mass="1332.2920" assumed_charge="3" index="8">
+    <search_result>      <search_hit hit_rank="1" peptide="MAAGENPAAEMIK" peptide_prev_aa="K" peptide_next_aa="S" protein="gi|16132265|ref|NP_418563.1|" num_tot_proteins="2" num_matched_ions=" 16" tot_num_ions=" 48" calc_neutral_pep_mass="1332.5920" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="1.058"/>
+        <search_score name="deltacn" value="0.191"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="177.5"/>
+        <search_score name="sprank" value="8"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1007.1007.1" start_scan="1007" end_scan="1007" precursor_neutral_mass="867.2920" assumed_charge="1" index="9">
+    <search_result>      <search_hit hit_rank="1" peptide="GALLHVEK" peptide_prev_aa="K" peptide_next_aa="M" protein="gi|16128020|ref|NP_414567.1|" num_tot_proteins="1" num_matched_ions="  4" tot_num_ions=" 14" calc_neutral_pep_mass="865.9920" massdiff="+1.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="0.467"/>
+        <search_score name="deltacn" value="0.011"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="39.4"/>
+        <search_score name="sprank" value="30"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1008.1008.2" start_scan="1008" end_scan="1008" precursor_neutral_mass="691.0920" assumed_charge="2" index="10">
+    <search_result>      <search_hit hit_rank="1" peptide="RLFTR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16130457|ref|NP_417027.1|" num_tot_proteins="1" num_matched_ions="  5" tot_num_ions="  8" calc_neutral_pep_mass="691.7920" massdiff="-0.7" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="0.903"/>
+        <search_score name="deltacn" value="0.333"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="172.8"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1008.1008.3" start_scan="1008" end_scan="1008" precursor_neutral_mass="1036.7920" assumed_charge="3" index="11">
+    <search_result>      <search_hit hit_rank="1" peptide="VHEGLNTLR" peptide_prev_aa="R" peptide_next_aa="L" protein="gi|16128370|ref|NP_414919.1|" num_tot_proteins="1" num_matched_ions="  6" tot_num_ions=" 32" calc_neutral_pep_mass="1038.1920" massdiff="-1.4" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="0.767"/>
+        <search_score name="deltacn" value="0.089"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="66.1"/>
+        <search_score name="sprank" value="18"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1010.1010.1" start_scan="1010" end_scan="1010" precursor_neutral_mass="869.4920" assumed_charge="1" index="12">
+    <search_result>      <search_hit hit_rank="1" peptide="HFRALVK" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|16130926|ref|NP_417502.1|" num_tot_proteins="1" num_matched_ions="  7" tot_num_ions=" 12" calc_neutral_pep_mass="870.0920" massdiff="-0.6" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
+        <search_score name="xcorr" value="0.995"/>
+        <search_score name="deltacn" value="0.065"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="152.2"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1011.1011.1" start_scan="1011" end_scan="1011" precursor_neutral_mass="734.4920" assumed_charge="1" index="13">
+    <search_result>      <search_hit hit_rank="1" peptide="FRDGLK" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|16132019|ref|NP_418618.1|" num_tot_proteins="1" num_matched_ions="  7" tot_num_ions=" 10" calc_neutral_pep_mass="734.8920" massdiff="-0.4" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
+        <search_score name="xcorr" value="1.467"/>
+        <search_score name="deltacn" value="0.396"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="140.5"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1012.1012.1" start_scan="1012" end_scan="1012" precursor_neutral_mass="899.3920" assumed_charge="1" index="14">
+    <search_result>      <search_hit hit_rank="1" peptide="RQLAERK" peptide_prev_aa="R" peptide_next_aa="Q" protein="gi|16129398|ref|NP_415956.1|" num_tot_proteins="1" num_matched_ions="  6" tot_num_ions=" 12" calc_neutral_pep_mass="899.9920" massdiff="-0.6" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="0.797"/>
+        <search_score name="deltacn" value="0.156"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="37.7"/>
+        <search_score name="sprank" value="8"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1014.1014.1" start_scan="1014" end_scan="1014" precursor_neutral_mass="869.5920" assumed_charge="1" index="15">
+    <search_result>      <search_hit hit_rank="1" peptide="HFRALVK" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|16130926|ref|NP_417502.1|" num_tot_proteins="1" num_matched_ions="  6" tot_num_ions=" 12" calc_neutral_pep_mass="870.0920" massdiff="-0.5" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
+        <search_score name="xcorr" value="0.908"/>
+        <search_score name="deltacn" value="0.005"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="110.4"/>
+        <search_score name="sprank" value="12"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1015.1015.1" start_scan="1015" end_scan="1015" precursor_neutral_mass="1077.9920" assumed_charge="1" index="16">
+    <search_result>      <search_hit hit_rank="1" peptide="KVYQLAETK" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|16128363|ref|NP_414912.1|" num_tot_proteins="1" num_matched_ions="  8" tot_num_ions=" 16" calc_neutral_pep_mass="1079.2920" massdiff="-1.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="0.897"/>
+        <search_score name="deltacn" value="0.056"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="125.1"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1016.1016.1" start_scan="1016" end_scan="1016" precursor_neutral_mass="871.6920" assumed_charge="1" index="17">
+    <search_result>      <search_hit hit_rank="1" peptide="VGAITAANR" peptide_prev_aa="K" peptide_next_aa="I" protein="gi|16129608|ref|NP_416167.1|" num_tot_proteins="1" num_matched_ions="  9" tot_num_ions=" 16" calc_neutral_pep_mass="871.9920" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="1.028"/>
+        <search_score name="deltacn" value="0.115"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="238.6"/>
+        <search_score name="sprank" value="1"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+    <spectrum_query spectrum="000.1018.1018.1" start_scan="1018" end_scan="1018" precursor_neutral_mass="919.7920" assumed_charge="1" index="18">
+    <search_result>      <search_hit hit_rank="1" peptide="DFLIATLK" peptide_prev_aa="K" peptide_next_aa="P" protein="gi|16131978|ref|NP_418577.1|" num_tot_proteins="1" num_matched_ions="  7" tot_num_ions=" 14" calc_neutral_pep_mass="920.0920" massdiff="-0.3" num_tol_term="1" num_missed_cleavages="0" is_rejected="0">
+        <search_score name="xcorr" value="1.010"/>
+        <search_score name="deltacn" value="0.156"/>
+        <search_score name="deltacnstar" value="0"/>
+        <search_score name="spscore" value="79.2"/>
+        <search_score name="sprank" value="7"/>
+      </search_hit>
+    </search_result>
+    </spectrum_query>
+  </msms_run_summary>
+</msms_pipeline_analysis>