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

mspire 0.2.4 → 0.3.0

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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/opd1_2runs_2mods/interact-opd1_mods__small.xml ADDED Viewed

@@ -0,0 +1,753 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?xml-stylesheet type="text/xsl" href="/work/tpp-data/interact-opd1_mods.xsl"?>
+<msms_pipeline_analysis date="2007-04-24T13:37:08" 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="/work/tpp-data/interact-opd1_mods.xml">
+    <analysis_summary analysis="database_refresh" time="2007-04-24T13:37:10"/>
+    <analysis_summary analysis="peptideprophet" time="2007-04-24T13:37:09">
+        <peptideprophet_summary version="PeptideProphet v3.0 April 1, 2004 (TPP v2.9 GALE rev.2, Build 200703091101)" author="AKeller@ISB" min_prob="0.05" options=" " est_tot_num_correct="623.8">
+            <inputfile name="/work/john/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/020"/>
+            <inputfile name="/work/john/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/040"/>
+            <roc_data_point min_prob="0.99" sensitivity="0.1070" error="0.0016" num_corr="63" num_incorr="0"/>
+            <roc_data_point min_prob="0.98" sensitivity="0.1154" error="0.0025" num_corr="68" num_incorr="0"/>
+            <roc_data_point min_prob="0.95" sensitivity="0.1319" error="0.0064" num_corr="78" num_incorr="0"/>
+            <roc_data_point min_prob="0.90" sensitivity="0.1760" error="0.0244" num_corr="103" num_incorr="3"/>
+            <roc_data_point min_prob="0.85" sensitivity="0.2312" error="0.0500" num_corr="136" num_incorr="7"/>
+            <roc_data_point min_prob="0.80" sensitivity="0.2605" error="0.0666" num_corr="153" num_incorr="11"/>
+            <roc_data_point min_prob="0.75" sensitivity="0.2934" error="0.0876" num_corr="172" num_incorr="17"/>
+            <roc_data_point min_prob="0.70" sensitivity="0.3342" error="0.1153" num_corr="196" num_incorr="26"/>
+            <roc_data_point min_prob="0.65" sensitivity="0.3870" error="0.1515" num_corr="227" num_incorr="41"/>
+            <roc_data_point min_prob="0.60" sensitivity="0.4561" error="0.1950" num_corr="268" num_incorr="65"/>
+            <roc_data_point min_prob="0.55" sensitivity="0.5004" error="0.2220" num_corr="294" num_incorr="84"/>
+            <roc_data_point min_prob="0.50" sensitivity="0.5440" error="0.2513" num_corr="320" num_incorr="107"/>
+            <roc_data_point min_prob="0.45" sensitivity="0.5885" error="0.2825" num_corr="346" num_incorr="136"/>
+            <roc_data_point min_prob="0.40" sensitivity="0.6306" error="0.3150" num_corr="371" num_incorr="170"/>
+            <roc_data_point min_prob="0.35" sensitivity="0.6862" error="0.3578" num_corr="403" num_incorr="225"/>
+            <roc_data_point min_prob="0.30" sensitivity="0.7326" error="0.3953" num_corr="431" num_incorr="281"/>
+            <roc_data_point min_prob="0.25" sensitivity="0.7787" error="0.4350" num_corr="458" num_incorr="352"/>
+            <roc_data_point min_prob="0.20" sensitivity="0.8284" error="0.4821" num_corr="487" num_incorr="453"/>
+            <roc_data_point min_prob="0.15" sensitivity="0.8621" error="0.5188" num_corr="507" num_incorr="546"/>
+            <roc_data_point min_prob="0.10" sensitivity="0.9117" error="0.5837" num_corr="536" num_incorr="751"/>
+            <roc_data_point min_prob="0.05" sensitivity="0.9552" error="0.6583" num_corr="561" num_incorr="1082"/>
+            <roc_data_point min_prob="0.00" sensitivity="1.0000" error="0.8753" num_corr="588" num_incorr="4123"/>
+            <error_point error="0.000" min_prob="1.00" num_corr="42" num_incorr="0"/>
+            <error_point error="0.010" min_prob="0.94" num_corr="84" num_incorr="1"/>
+            <error_point error="0.020" min_prob="0.92" num_corr="99" num_incorr="2"/>
+            <error_point error="0.025" min_prob="0.90" num_corr="105" num_incorr="3"/>
+            <error_point error="0.030" min_prob="0.89" num_corr="111" num_incorr="4"/>
+            <error_point error="0.040" min_prob="0.87" num_corr="125" num_incorr="5"/>
+            <error_point error="0.050" min_prob="0.84" num_corr="138" num_incorr="7"/>
+            <error_point error="0.075" min_prob="0.78" num_corr="163" num_incorr="13"/>
+            <error_point error="0.100" min_prob="0.73" num_corr="184" num_incorr="21"/>
+            <distribution_point fvalue="-4.90" obs_1_distr="7" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="14" model_2_pos_distr="0.00" model_2_neg_distr="0.01" obs_3_distr="5" model_3_pos_distr="0.02" model_3_neg_distr="0.00"/>
+            <distribution_point fvalue="-4.70" obs_1_distr="9" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="22" model_2_pos_distr="0.00" model_2_neg_distr="0.34" obs_3_distr="5" model_3_pos_distr="0.02" model_3_neg_distr="0.00"/>
+            <distribution_point fvalue="-4.50" obs_1_distr="13" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="8" model_2_pos_distr="0.00" model_2_neg_distr="1.76" obs_3_distr="7" model_3_pos_distr="0.03" model_3_neg_distr="0.04"/>
+            <distribution_point fvalue="-4.30" obs_1_distr="10" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="23" model_2_pos_distr="0.00" model_2_neg_distr="4.92" obs_3_distr="8" model_3_pos_distr="0.04" model_3_neg_distr="0.23"/>
+            <distribution_point fvalue="-4.10" obs_1_distr="10" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="19" model_2_pos_distr="0.00" model_2_neg_distr="10.02" obs_3_distr="10" model_3_pos_distr="0.06" model_3_neg_distr="0.86"/>
+            <distribution_point fvalue="-3.90" obs_1_distr="28" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="15" model_2_pos_distr="0.01" model_2_neg_distr="16.82" obs_3_distr="6" model_3_pos_distr="0.08" model_3_neg_distr="2.28"/>
+            <distribution_point fvalue="-3.70" obs_1_distr="15" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="17" model_2_pos_distr="0.01" model_2_neg_distr="24.79" obs_3_distr="10" model_3_pos_distr="0.10" model_3_neg_distr="4.90"/>
+            <distribution_point fvalue="-3.50" obs_1_distr="25" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="29" model_2_pos_distr="0.02" model_2_neg_distr="33.30" obs_3_distr="16" model_3_pos_distr="0.14" model_3_neg_distr="8.99"/>
+            <distribution_point fvalue="-3.30" obs_1_distr="15" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="26" model_2_pos_distr="0.03" model_2_neg_distr="41.69" obs_3_distr="14" model_3_pos_distr="0.18" model_3_neg_distr="14.67"/>
+            <distribution_point fvalue="-3.10" obs_1_distr="28" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="46" model_2_pos_distr="0.05" model_2_neg_distr="49.42" obs_3_distr="20" model_3_pos_distr="0.24" model_3_neg_distr="21.82"/>
+            <distribution_point fvalue="-2.90" obs_1_distr="28" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="33" model_2_pos_distr="0.07" model_2_neg_distr="56.08" obs_3_distr="28" model_3_pos_distr="0.31" model_3_neg_distr="30.13"/>
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+                        <parameter name="ntt=2" value="1.000"/>
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+                <mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
+                    <posmodel_distribution>
+                        <parameter name="nmc=0" value="0.739"/>
+                        <parameter name="1&lt;=nmc&lt;=2" value="0.261"/>
+                        <parameter name="nmc&gt;=3" value="0.000"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="nmc=0" value="0.566"/>
+                        <parameter name="1&lt;=nmc&lt;=2" value="0.434"/>
+                        <parameter name="nmc&gt;=3" value="0.000"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+                <mixturemodel_distribution name="var offset mass diff [massd] (offset: 0.000000)">
+                    <posmodel_distribution>
+                        <parameter name="massd=0.000000" value="1.000000000"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="massd=0.000000" value="1.000000000"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+            </mixture_model>
+            <mixture_model precursor_ion_charge="2" comments="using training data negative distributions" prior_probability="0.115" est_tot_correct="196.3" tot_num_spectra="1706" num_iterations="5">
+                <mixturemodel_distribution name="SEQUEST discrim score [fval]	negmean: -3.25">
+                    <posmodel_distribution type="gaussian">
+                        <parameter name="mean" value="1.89"/>
+                        <parameter name="stdev" value="1.52"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution type="gamma">
+                        <parameter name="m1" value="3.69"/>
+                        <parameter name="m2" value="16.40"/>
+                        <parameter name="alpha" value="0.75"/>
+                        <parameter name="beta" value="4.94"/>
+                        <parameter name="zero" value="-5.00"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+                <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]">
+                    <posmodel_distribution>
+                        <parameter name="ntt=0" value="0.000"/>
+                        <parameter name="ntt=1" value="0.000"/>
+                        <parameter name="ntt=2" value="1.000"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="ntt=0" value="0.000"/>
+                        <parameter name="ntt=1" value="0.000"/>
+                        <parameter name="ntt=2" value="1.000"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+                <mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
+                    <posmodel_distribution>
+                        <parameter name="nmc=0" value="0.385"/>
+                        <parameter name="1&lt;=nmc&lt;=2" value="0.615"/>
+                        <parameter name="nmc&gt;=3" value="0.000"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="nmc=0" value="0.437"/>
+                        <parameter name="1&lt;=nmc&lt;=2" value="0.563"/>
+                        <parameter name="nmc&gt;=3" value="0.000"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+                <mixturemodel_distribution name="var offset mass diff [massd] (offset: -0.500000)">
+                    <posmodel_distribution>
+                        <parameter name="massd=0.000000" value="0.539533203"/>
+                        <parameter name="massd=1.000000" value="0.460466797"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="massd=0.000000" value="0.496137305"/>
+                        <parameter name="massd=1.000000" value="0.503862695"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+            </mixture_model>
+            <mixture_model precursor_ion_charge="3" comments="using training data negative distributions" prior_probability="0.201" est_tot_correct="423.7" tot_num_spectra="2107" num_iterations="3">
+                <mixturemodel_distribution name="SEQUEST discrim score [fval]	negmean: -2.85">
+                    <posmodel_distribution type="gaussian">
+                        <parameter name="mean" value="3.13"/>
+                        <parameter name="stdev" value="2.15"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution type="gamma">
+                        <parameter name="m1" value="4.44"/>
+                        <parameter name="m2" value="22.22"/>
+                        <parameter name="alpha" value="0.58"/>
+                        <parameter name="beta" value="7.71"/>
+                        <parameter name="zero" value="-5.00"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+                <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]">
+                    <posmodel_distribution>
+                        <parameter name="ntt=0" value="0.000"/>
+                        <parameter name="ntt=1" value="0.000"/>
+                        <parameter name="ntt=2" value="1.000"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="ntt=0" value="0.000"/>
+                        <parameter name="ntt=1" value="0.000"/>
+                        <parameter name="ntt=2" value="1.000"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+                <mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
+                    <posmodel_distribution>
+                        <parameter name="nmc=0" value="0.310"/>
+                        <parameter name="1&lt;=nmc&lt;=2" value="0.690"/>
+                        <parameter name="nmc&gt;=3" value="0.000"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="nmc=0" value="0.292"/>
+                        <parameter name="1&lt;=nmc&lt;=2" value="0.708"/>
+                        <parameter name="nmc&gt;=3" value="0.000"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+                <mixturemodel_distribution name="var offset mass diff [massd] (offset: 0.000000)">
+                    <posmodel_distribution>
+                        <parameter name="massd=0.000000" value="1.000000000"/>
+                    </posmodel_distribution>
+                    <negmodel_distribution>
+                        <parameter name="massd=0.000000" value="1.000000000"/>
+                    </negmodel_distribution>
+                </mixturemodel_distribution>
+            </mixture_model>
+        </peptideprophet_summary>
+    </analysis_summary>
+    <analysis_summary analysis="interact" time="2007-04-24T13:37:06">
+        <interact_summary filename="/work/tpp-data/interact-opd1_mods.xml" directory="/work/tpp-data">
+            <inputfile name="sequest/pepxml/020.xml"/>
+            <inputfile name="sequest/pepxml/040.xml"/>
+        </interact_summary>
+    </analysis_summary>
+    <dataset_derivation generation_no="0"/>
+    <msms_run_summary base_name="/work/john/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/020" msManufacturer="ThermoFinnigan" msModel="LCQ Deca XP" 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/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/020" 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="/project/marcotte/marcotte/ms/database/ecoli_K12_ncbi_20060321.fasta" type="AA"/>
+            <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/>
+            <aminoacid_modification binary="N" mass="147.192" symbol="*" massdiff="+15.9994" aminoacid="M" variable="Y"/>
+            <aminoacid_modification binary="N" mass="167.0581" symbol="#" massdiff="+79.9799" aminoacid="S" variable="Y"/>
+            <aminoacid_modification binary="N" mass="181.085" symbol="#" massdiff="+79.9799" aminoacid="T" variable="Y"/>
+            <aminoacid_modification binary="N" mass="243.1559" symbol="#" massdiff="+79.9799" aminoacid="Y" variable="Y"/>
+            <parameter name="diff_search_options" value="15.999400 M 79.979900 STY 0.000000 M 0.000000 X 0.000000 T 0.000000 Y"/>
+            <parameter name="digest_mass_range" value="600.0 3500.0"/>
+            <parameter name="enzyme_info" value="Trypsin(KR/P) 1 1 KR P"/>
+            <parameter name="first_database_name" value="/project/marcotte/marcotte/ms/database/ecoli_K12_ncbi_20060321.fasta"/>
+            <parameter name="fragment_ion_tolerance" value="1.0000"/>
+            <parameter name="fragment_ion_units" value="0"/>
+            <parameter name="ion_cutoff_percentage" value="0.0000"/>
+            <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="mass_type_fragment" value="0"/>
+            <parameter name="mass_type_parent" value="0"/>
+            <parameter name="match_peak_allowed_error" value="1"/>
+            <parameter name="match_peak_count" value="0"/>
+            <parameter name="match_peak_tolerance" value="1.0000"/>
+            <parameter name="max_num_differential_per_peptide" value="3"/>
+            <parameter name="max_num_internal_cleavage_sites" value="2"/>
+            <parameter name="normalize_xcorr" value="0"/>
+            <parameter name="nucleotide_reading_frame" value="0"/>
+            <parameter name="num_description_lines" value="5"/>
+            <parameter name="num_output_lines" value="10"/>
+            <parameter name="num_results" value="250"/>
+            <parameter name="partial_sequence" value=""/>
+            <parameter name="peptide_mass_tolerance" value="25.0000"/>
+            <parameter name="peptide_mass_units" value="2"/>
+            <parameter name="print_duplicate_references" value="40"/>
+            <parameter name="protein_mass_filter" value="0 0"/>
+            <parameter name="remove_precursor_peak" value="0"/>
+            <parameter name="search_engine" value="SEQUEST"/>
+            <parameter name="second_database_name" value=""/>
+            <parameter name="sequence_header_filter" value=""/>
+            <parameter name="show_fragment_ions" value="0"/>
+            <parameter name="term_diff_search_options" value="0.000000 0.000000"/>
+        </search_summary>
+        <analysis_timestamp analysis="database_refresh" time="2007-04-24T13:37:10" id="1">
+            <database_refresh_timestamp database="/project/marcotte/marcotte/ms/database/ecoli_K12_ncbi_20060321.fasta"/>
+        </analysis_timestamp>
+        <analysis_timestamp analysis="peptideprophet" time="2007-04-24T13:37:09" id="1"/>
+        <spectrum_query spectrum="020.42.42.3" start_scan="42" end_scan="42" precursor_neutral_mass="1015.77285654469" assumed_charge="3" index="1">
+            <search_result>
+                <search_hit hit_rank="1" peptide="GTGVSVTR" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|49176370|ref|YP_026228.1|" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="70" calc_neutral_pep_mass="1015.79382542" massdiff="-0.0209688753124055" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="putative outer membrane protein [Escherichia coli K12]">
+                    <modification_info modified_peptide="GT[181]GVSV[167]TR">
+                        <mod_aminoacid_mass position="2" mass="181.085"/>
+                        <mod_aminoacid_mass position="6" mass="167.0581"/>
+                        <mod_aminoacid_mass position="9" mass="181.085"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="1.06543827056885"/>
+                    <search_score name="deltacn" value="0.192325830459595"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="77.8397979736328"/>
+                    <search_score name="sprank" value="3"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.07881571" all_ntt_prob="(0.0000,0.0000,0.0788)">
+                            <search_score_summary>
+                                <parameter name="fval" value="0.1592"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="-0.021"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.58.58.3" start_scan="58" end_scan="58" precursor_neutral_mass="2586.0981739275" assumed_charge="3" index="2">
+            <search_result>
+                <search_hit hit_rank="1" peptide="AVAAMTRYRQQLLPPLFSALMK" peptide_prev_aa="R" peptide_next_aa="Y" protein="gi|16131943|ref|NP_418541.1|" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="126" calc_neutral_pep_mass="2586.03404942" massdiff="+0.0641245075007646" num_tol_term="2" num_missed_cleavages="2" is_rejected="0" protein_descr="arginine decarboxylase; inducible by acid, catabolic [Escherichia coli K12]">
+                    <modification_info modified_peptide="AVAAMTRYRQQLLPPLFS[167]ALMK">
+                        <mod_aminoacid_mass position="18" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.223117798566818"/>
+                    <search_score name="deltacn" value="0.644854307174683"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="15.7188243865967"/>
+                    <search_score name="sprank" value="8"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.25764597" all_ntt_prob="(0.0000,0.0000,0.2576)">
+                            <search_score_summary>
+                                <parameter name="fval" value="1.2777"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="0.064"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.80.80.2" start_scan="80" end_scan="80" precursor_neutral_mass="795.857037471563" assumed_charge="2" index="3">
+            <search_result>
+                <search_hit hit_rank="1" peptide="YVPPIK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|16129101|ref|NP_415656.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="15" calc_neutral_pep_mass="795.86332542" massdiff="-0.00628794843748892" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="e14 prophage [Escherichia coli K12]">
+                    <modification_info modified_peptide="Y[243]VPPIK">
+                        <mod_aminoacid_mass position="1" mass="243.1559"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.705689549446106"/>
+                    <search_score name="deltacn" value="0.395860612392426"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="152.141448974609"/>
+                    <search_score name="sprank" value="1"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.11128366" all_ntt_prob="(0.0000,0.0000,0.1113)">
+                            <search_score_summary>
+                                <parameter name="fval" value="0.0939"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="-0.006"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.104.104.3" start_scan="104" end_scan="104" precursor_neutral_mass="1326.28677256031" assumed_charge="3" index="4">
+            <search_result>
+                <search_hit hit_rank="1" peptide="LEGEESDLARK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131046|ref|NP_417623.1|" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="60" calc_neutral_pep_mass="1326.30978542" massdiff="-0.0230128596874692" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="hypothetical protein b3154 [Escherichia coli K12]">
+                    <modification_info modified_peptide="LEGEES[167]DLARK">
+                        <mod_aminoacid_mass position="6" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.994660556316376"/>
+                    <search_score name="deltacn" value="0.397965431213379"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="120.155563354492"/>
+                    <search_score name="sprank" value="8"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.46972454" all_ntt_prob="(0.0000,0.0000,0.4697)">
+                            <search_score_summary>
+                                <parameter name="fval" value="2.0617"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="-0.023"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.158.158.3" start_scan="158" end_scan="158" precursor_neutral_mass="1151.46792490406" assumed_charge="3" index="5">
+            <search_result>
+                <search_hit hit_rank="1" peptide="MKDLLKFLK" peptide_prev_aa="-" peptide_next_aa="A" protein="gi|16131818|ref|NP_418415.1|" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="32" calc_neutral_pep_mass="1151.46772442" massdiff="+0.000200484062816031" num_tol_term="2" num_missed_cleavages="2" is_rejected="0" protein_descr="DNA-directed RNA polymerase beta' subunit [Escherichia coli K12]">
+                    <modification_info modified_peptide="M[147]KDLLKFLK">
+                        <mod_aminoacid_mass position="1" mass="147.192"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.254981607198715"/>
+                    <search_score name="deltacn" value="0.720395803451538"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="51.8907661437988"/>
+                    <search_score name="sprank" value="1"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.47041741" all_ntt_prob="(0.0000,0.0000,0.4704)">
+                            <search_score_summary>
+                                <parameter name="fval" value="2.0641"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="0.000"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.171.171.3" start_scan="171" end_scan="171" precursor_neutral_mass="1413.41805918141" assumed_charge="3" index="6">
+            <search_result>
+                <search_hit hit_rank="1" peptide="TLAAFLYALDR" peptide_prev_aa="K" peptide_next_aa="L" protein="gi|16129611|ref|NP_416170.1|" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="80" calc_neutral_pep_mass="1413.41179042" massdiff="+0.00626876140631794" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="member of ATP-dependent helicase superfamily II [Escherichia coli K12]">
+                    <modification_info modified_peptide="T[181]LAAFLYA[243]LDR">
+                        <mod_aminoacid_mass position="1" mass="181.085"/>
+                        <mod_aminoacid_mass position="8" mass="243.1559"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.654914498329163"/>
+                    <search_score name="deltacn" value="0.441779345273972"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="49.6860275268555"/>
+                    <search_score name="sprank" value="30"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.21833146" all_ntt_prob="(0.0000,0.0000,0.2183)">
+                            <search_score_summary>
+                                <parameter name="fval" value="1.1016"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="0.006"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.187.187.3" start_scan="187" end_scan="187" precursor_neutral_mass="1721.90920908375" assumed_charge="3" index="7">
+            <search_result>
+                <search_hit hit_rank="1" peptide="GLIQLANMLRSQAAR" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|90111091|ref|NP_414689.4|" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="84" calc_neutral_pep_mass="1721.92441442" massdiff="-0.0152053362498918" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="2'-5' RNA ligase [Escherichia coli K12]">
+                    <modification_info modified_peptide="GLIQLANMLRS[167]QAAR">
+                        <mod_aminoacid_mass position="11" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.896096765995026"/>
+                    <search_score name="deltacn" value="0.253862977027893"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="130.671142578125"/>
+                    <search_score name="sprank" value="2"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.11045808" all_ntt_prob="(0.0000,0.0000,0.1105)">
+                            <search_score_summary>
+                                <parameter name="fval" value="0.4545"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="-0.015"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.207.207.3" start_scan="207" end_scan="207" precursor_neutral_mass="1015.905791115" assumed_charge="3" index="8">
+            <search_result>
+                <search_hit hit_rank="1" peptide="TVETSDER" peptide_prev_aa="K" peptide_next_aa="L" protein="gi|16131359|ref|NP_417944.1|" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="42" calc_neutral_pep_mass="1015.91629342" massdiff="-0.0105023050000455" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="hypothetical protein b3487 [Escherichia coli K12]">
+                    <modification_info modified_peptide="TVETS[167]DER">
+                        <mod_aminoacid_mass position="5" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.695196807384491"/>
+                    <search_score name="deltacn" value="0.263394951820374"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="105.548156738281"/>
+                    <search_score name="sprank" value="1"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.05621524" all_ntt_prob="(0.0000,0.0000,0.0562)">
+                            <search_score_summary>
+                                <parameter name="fval" value="-0.1293"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="-0.011"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.210.210.3" start_scan="210" end_scan="210" precursor_neutral_mass="977.813811134531" assumed_charge="3" index="9">
+            <search_result>
+                <search_hit hit_rank="1" peptide="VNGGSTQR" peptide_prev_aa="R" peptide_next_aa="K" protein="gi|16129784|ref|NP_416344.1|" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="56" calc_neutral_pep_mass="977.81090142" massdiff="+0.00290971453125621" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="carboxy-terminal protease for penicillin-binding protein 3 [Escherichia coli K12]">
+                    <modification_info modified_peptide="VNGGS[167]TQ[181]R">
+                        <mod_aminoacid_mass position="5" mass="167.0581"/>
+                        <mod_aminoacid_mass position="7" mass="181.085"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.344329476356506"/>
+                    <search_score name="deltacn" value="0.82324880361557"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="57.4015884399414"/>
+                    <search_score name="sprank" value="4"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.83586426" all_ntt_prob="(0.0000,0.0000,0.8359)">
+                            <search_score_summary>
+                                <parameter name="fval" value="3.7233"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="0.003"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.228.228.3" start_scan="228" end_scan="228" precursor_neutral_mass="903.86721689625" assumed_charge="3" index="10">
+            <search_result>
+                <search_hit hit_rank="1" peptide="TPVHNTR" peptide_prev_aa="K" peptide_next_aa="-" protein="gi|16130577|ref|NP_417149.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="36" calc_neutral_pep_mass="903.88037542" massdiff="-0.0131585237500076" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="gamma-aminobutyrate transport protein, RpoS-dependent (APC family) [Escherichia coli K12]">
+                    <modification_info modified_peptide="T[181]PVHNTR">
+                        <mod_aminoacid_mass position="1" mass="181.085"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.582937955856323"/>
+                    <search_score name="deltacn" value="0.484805673360825"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="111.365089416504"/>
+                    <search_score name="sprank" value="2"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.34234940" all_ntt_prob="(0.0000,0.0000,0.3423)">
+                            <search_score_summary>
+                                <parameter name="fval" value="1.6114"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="-0.013"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.280.280.2" start_scan="280" end_scan="280" precursor_neutral_mass="789.701031612188" assumed_charge="2" index="11">
+            <search_result>
+                <search_hit hit_rank="1" peptide="SSSSTNK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|90111655|ref|NP_418298.4|" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="18" calc_neutral_pep_mass="789.68607542" massdiff="+0.0149561921874692" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="putative GTP-binding protein [Escherichia coli K12]">
+                    <modification_info modified_peptide="S[167]SSSTNK">
+                        <mod_aminoacid_mass position="1" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.543601095676422"/>
+                    <search_score name="deltacn" value="0.520685315132141"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="26.5204181671143"/>
+                    <search_score name="sprank" value="3"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.08176422" all_ntt_prob="(0.0000,0.0000,0.0818)">
+                            <search_score_summary>
+                                <parameter name="fval" value="-0.0548"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="0.015"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.290.290.3" start_scan="290" end_scan="290" precursor_neutral_mass="1775.8579395525" assumed_charge="3" index="12">
+            <search_result>
+                <search_hit hit_rank="1" peptide="KEDGASKNTSMTSVLK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|16131714|ref|NP_418310.1|" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="90" calc_neutral_pep_mass="1775.87765042" massdiff="-0.0197108675004074" num_tol_term="2" num_missed_cleavages="2" is_rejected="0" protein_descr="putative resistance protein (transport) [Escherichia coli K12]">
+                    <modification_info modified_peptide="KEDGAS[167]KNTSMTSVLK">
+                        <mod_aminoacid_mass position="6" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.71731048822403"/>
+                    <search_score name="deltacn" value="0.346047312021255"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="71.4732513427734"/>
+                    <search_score name="sprank" value="43"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.09169276" all_ntt_prob="(0.0000,0.0000,0.0917)">
+                            <search_score_summary>
+                                <parameter name="fval" value="0.2904"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="-0.020"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.292.292.3" start_scan="292" end_scan="292" precursor_neutral_mass="1029.88882334156" assumed_charge="3" index="13">
+            <search_result>
+                <search_hit hit_rank="1" peptide="ESDSLEDR" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|16128320|ref|NP_414869.1|" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="42" calc_neutral_pep_mass="1029.89982942" massdiff="-0.0110060784375037" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="putative acetyl-CoA synthetase of the propionate catabolism operon [Escherichia coli K12]">
+                    <modification_info modified_peptide="ESDS[167]LEDR">
+                        <mod_aminoacid_mass position="4" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.324827522039413"/>
+                    <search_score name="deltacn" value="0.705897331237793"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="106.849151611328"/>
+                    <search_score name="sprank" value="1"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.59508077" all_ntt_prob="(0.0000,0.0000,0.5951)">
+                            <search_score_summary>
+                                <parameter name="fval" value="2.5088"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="-0.011"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.294.294.3" start_scan="294" end_scan="294" precursor_neutral_mass="913.180876564219" assumed_charge="3" index="14">
+            <search_result>
+                <search_hit hit_rank="1" peptide="MFGKKMR" peptide_prev_aa="R" peptide_next_aa="H" protein="gi|16130783|ref|NP_417357.1|" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="24" calc_neutral_pep_mass="913.16718242" massdiff="+0.0136941442189027" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="possible hypoxanthine oxidase [Escherichia coli K12]">
+                    <modification_info modified_peptide="M[147]FGKKMR">
+                        <mod_aminoacid_mass position="1" mass="147.192"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.792168140411377"/>
+                    <search_score name="deltacn" value="0.886182427406311"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="99.004280090332"/>
+                    <search_score name="sprank" value="1"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="1.00000000" all_ntt_prob="(0.0000,0.0000,1.0000)">
+                            <search_score_summary>
+                                <parameter name="fval" value="7.2590"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="0.014"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.295.295.3" start_scan="295" end_scan="295" precursor_neutral_mass="1022.85043222828" assumed_charge="3" index="15">
+            <search_result>
+                <search_hit hit_rank="1" peptide="DKAGTDTR" peptide_prev_aa="K" peptide_next_aa="F" protein="gi|16129247|ref|NP_415802.1|" num_tot_proteins="1" num_matched_ions="13" tot_num_ions="56" calc_neutral_pep_mass="1022.84844242" massdiff="+0.00198980828133699" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="exoribonuclease II [Escherichia coli K12]">
+                    <modification_info modified_peptide="DKAGT[181]DTR[181]">
+                        <mod_aminoacid_mass position="5" mass="181.085"/>
+                        <mod_aminoacid_mass position="8" mass="181.085"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.570928752422333"/>
+                    <search_score name="deltacn" value="0.741859972476959"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="189.744049072266"/>
+                    <search_score name="sprank" value="1"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.91871789" all_ntt_prob="(0.0000,0.0000,0.9187)">
+                            <search_score_summary>
+                                <parameter name="fval" value="4.6526"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="0.002"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.299.299.2" start_scan="299" end_scan="299" precursor_neutral_mass="1851.2031068075" assumed_charge="2" index="16">
+            <search_result>
+                <search_hit hit_rank="1" peptide="IVPLIAYMSKFFTLK" peptide_prev_aa="K" peptide_next_aa="A" protein="gi|16129143|ref|NP_415698.1|" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="42" calc_neutral_pep_mass="1851.20196942" massdiff="+0.00113738749996628" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="putative isomerase [Escherichia coli K12]">
+                    <modification_info modified_peptide="IVPLIAY[243]MSKFFTLK">
+                        <mod_aminoacid_mass position="7" mass="243.1559"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.68244069814682"/>
+                    <search_score name="deltacn" value="0.688492655754089"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="20.3025856018066"/>
+                    <search_score name="sprank" value="1"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.60240568" all_ntt_prob="(0.0000,0.0000,0.6024)">
+                            <search_score_summary>
+                                <parameter name="fval" value="2.4950"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="0.001"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.319.319.2" start_scan="319" end_scan="319" precursor_neutral_mass="701.73191540125" assumed_charge="2" index="17">
+            <search_result>
+                <search_hit hit_rank="1" peptide="MATATK" peptide_prev_aa="K" peptide_next_aa="T" protein="gi|16129160|ref|NP_415715.1|" num_tot_proteins="1" num_matched_ions="3" tot_num_ions="15" calc_neutral_pep_mass="701.73020542" massdiff="+0.00170998124997368" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="trehalase, periplasmic [Escherichia coli K12]">
+                    <modification_info modified_peptide="MAT[181]ATK">
+                        <mod_aminoacid_mass position="3" mass="181.085"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="0.471073925495148"/>
+                    <search_score name="deltacn" value="0.653317809104919"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="8.99399089813232"/>
+                    <search_score name="sprank" value="10"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.08904475" all_ntt_prob="(0.0000,0.0000,0.0890)">
+                            <search_score_summary>
+                                <parameter name="fval" value="0.0069"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="0"/>
+                                <parameter name="massd" value="0.002"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+        <spectrum_query spectrum="020.344.344.3" start_scan="344" end_scan="344" precursor_neutral_mass="1447.6040333025" assumed_charge="3" index="18">
+            <search_result>
+                <search_hit hit_rank="1" peptide="VAALRVPGGASLTR" peptide_prev_aa="R" peptide_next_aa="K" protein="gi|16129819|ref|NP_416380.1|" num_tot_proteins="1" num_matched_ions="16" tot_num_ions="78" calc_neutral_pep_mass="1447.58289842" massdiff="+0.0211348825000641" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="aspartyl-tRNA synthetase [Escherichia coli K12]">
+                    <modification_info modified_peptide="VAALRVPGGAS[167]LTR">
+                        <mod_aminoacid_mass position="11" mass="167.0581"/>
+                    </modification_info>
+                    <search_score name="xcorr" value="1.3090912103653"/>
+                    <search_score name="deltacn" value="0.259967535734177"/>
+                    <search_score name="deltacnstar" value="0"/>
+                    <search_score name="spscore" value="118.513412475586"/>
+                    <search_score name="sprank" value="4"/>
+                    <analysis_result analysis="peptideprophet">
+                        <peptideprophet_result probability="0.27738378" all_ntt_prob="(0.0000,0.0000,0.2774)">
+                            <search_score_summary>
+                                <parameter name="fval" value="1.3810"/>
+                                <parameter name="ntt" value="2"/>
+                                <parameter name="nmc" value="1"/>
+                                <parameter name="massd" value="0.021"/>
+                            </search_score_summary>
+                        </peptideprophet_result>
+                    </analysis_result>
+                </search_hit>
+            </search_result>
+        </spectrum_query>
+    </msms_run_summary>
+</msms_pipeline_analysis>