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/4-03-03_small.xml ADDED Viewed

@@ -0,0 +1,3876 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE msms_pipeline_analysis SYSTEM "/usr/bin/msms_analysis3.dtd">
+<?xml-stylesheet type="text/xsl" href="/var/www/html/isb/interact-4-03-03.xsl"?>
+<?xml-stylesheet type="text/xsl" href="/isb/std_xsl/pepXML_std.xsl"?>
+<msms_pipeline_analysis date="Wed Jun 14 15:46:49 2006" summary_xml="/var/www/html/isb/interact-4-03-03.xml">
+<peptideprophet_summary version="PeptideProphet v3.0 April 1, 2004" author="AKeller@ISB" inputfiles="/work/john/mult_align/exp/sequest/4-03-03/000 /work/john/mult_align/exp/sequest/4-03-03/020 /work/john/mult_align/exp/sequest/4-03-03/040 /work/john/mult_align/exp/sequest/4-03-03/060 /work/john/mult_align/exp/sequest/4-03-03/080 /work/john/mult_align/exp/sequest/4-03-03/100 /work/john/mult_align/exp/sequest/4-03-03/150 /work/john/mult_align/exp/sequest/4-03-03/200 /work/john/mult_align/exp/sequest/4-03-03/300 /work/john/mult_align/exp/sequest/4-03-03/500 /work/john/mult_align/exp/sequest/4-03-03/900" min_prob="0.05" options=" " est_tot_num_correct="1081.6">
+<peptideprophet_timestamp time="Wed Jun 14 15:59:16 2006"/>
+<roc_data_point min_prob="0.99" sensitivity="0.3592" error="0.0030" num_corr="386" num_incorr="1"/>
+<roc_data_point min_prob="0.98" sensitivity="0.4501" error="0.0053" num_corr="483" num_incorr="3"/>
+<roc_data_point min_prob="0.95" sensitivity="0.5635" error="0.0110" num_corr="605" num_incorr="7"/>
+<roc_data_point min_prob="0.90" sensitivity="0.6602" error="0.0205" num_corr="709" num_incorr="15"/>
+<roc_data_point min_prob="0.85" sensitivity="0.7198" error="0.0299" num_corr="773" num_incorr="24"/>
+<roc_data_point min_prob="0.80" sensitivity="0.7520" error="0.0372" num_corr="808" num_incorr="31"/>
+<roc_data_point min_prob="0.75" sensitivity="0.7737" error="0.0437" num_corr="831" num_incorr="38"/>
+<roc_data_point min_prob="0.70" sensitivity="0.7975" error="0.0525" num_corr="857" num_incorr="47"/>
+<roc_data_point min_prob="0.65" sensitivity="0.8151" error="0.0606" num_corr="875" num_incorr="57"/>
+<roc_data_point min_prob="0.60" sensitivity="0.8304" error="0.0690" num_corr="892" num_incorr="66"/>
+<roc_data_point min_prob="0.55" sensitivity="0.8471" error="0.0801" num_corr="910" num_incorr="79"/>
+<roc_data_point min_prob="0.50" sensitivity="0.8636" error="0.0933" num_corr="928" num_incorr="95"/>
+<roc_data_point min_prob="0.45" sensitivity="0.8791" error="0.1076" num_corr="944" num_incorr="114"/>
+<roc_data_point min_prob="0.40" sensitivity="0.8886" error="0.1179" num_corr="954" num_incorr="128"/>
+<roc_data_point min_prob="0.35" sensitivity="0.8973" error="0.1294" num_corr="964" num_incorr="143"/>
+<roc_data_point min_prob="0.30" sensitivity="0.9126" error="0.1536" num_corr="980" num_incorr="178"/>
+<roc_data_point min_prob="0.25" sensitivity="0.9232" error="0.1737" num_corr="992" num_incorr="208"/>
+<roc_data_point min_prob="0.20" sensitivity="0.9322" error="0.1945" num_corr="1001" num_incorr="242"/>
+<roc_data_point min_prob="0.15" sensitivity="0.9427" error="0.2265" num_corr="1013" num_incorr="296"/>
+<roc_data_point min_prob="0.10" sensitivity="0.9529" error="0.2689" num_corr="1024" num_incorr="376"/>
+<roc_data_point min_prob="0.05" sensitivity="0.9690" error="0.3654" num_corr="1041" num_incorr="599"/>
+<roc_data_point min_prob="0.00" sensitivity="1.0000" error="0.9686" num_corr="1074" num_incorr="33078"/>
+<error_point error="0.000" min_prob="1.00" num_corr="57" num_incorr="0"/>
+<error_point error="0.010" min_prob="0.96" num_corr="590" num_incorr="6"/>
+<error_point error="0.020" min_prob="0.90" num_corr="706" num_incorr="15"/>
+<error_point error="0.025" min_prob="0.88" num_corr="744" num_incorr="19"/>
+<error_point error="0.030" min_prob="0.85" num_corr="775" num_incorr="24"/>
+<error_point error="0.040" min_prob="0.78" num_corr="820" num_incorr="34"/>
+<error_point error="0.050" min_prob="0.72" num_corr="851" num_incorr="45"/>
+<error_point error="0.075" min_prob="0.58" num_corr="903" num_incorr="74"/>
+<error_point error="0.100" min_prob="0.48" num_corr="936" num_incorr="105"/>
+<distribution_point fvalue="-4.90" obs_1_distr="18" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="21" model_2_pos_distr="0.00" model_2_neg_distr="0.00" obs_3_distr="1" model_3_pos_distr="0.00" model_3_neg_distr="0.00"/>
+<distribution_point fvalue="-4.70" obs_1_distr="12" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="45" model_2_pos_distr="0.00" model_2_neg_distr="0.07" obs_3_distr="1" model_3_pos_distr="0.00" model_3_neg_distr="0.00"/>
+<distribution_point fvalue="-4.50" obs_1_distr="19" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="49" model_2_pos_distr="0.00" model_2_neg_distr="1.13" obs_3_distr="2" model_3_pos_distr="0.00" model_3_neg_distr="0.01"/>
+<distribution_point fvalue="-4.30" obs_1_distr="18" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="86" model_2_pos_distr="0.00" model_2_neg_distr="6.87" obs_3_distr="4" model_3_pos_distr="0.00" model_3_neg_distr="0.11"/>
+<distribution_point fvalue="-4.10" obs_1_distr="21" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="114" model_2_pos_distr="0.00" model_2_neg_distr="24.53" obs_3_distr="5" model_3_pos_distr="0.00" model_3_neg_distr="0.72"/>
+<distribution_point fvalue="-3.90" obs_1_distr="32" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="138" model_2_pos_distr="0.00" model_2_neg_distr="63.14" obs_3_distr="15" model_3_pos_distr="0.00" model_3_neg_distr="2.91"/>
+<distribution_point fvalue="-3.70" obs_1_distr="37" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="190" model_2_pos_distr="0.00" model_2_neg_distr="130.13" obs_3_distr="17" model_3_pos_distr="0.00" model_3_neg_distr="8.61"/>
+<distribution_point fvalue="-3.50" obs_1_distr="51" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="228" model_2_pos_distr="0.00" model_2_neg_distr="228.42" obs_3_distr="25" model_3_pos_distr="0.00" model_3_neg_distr="20.41"/>
+<distribution_point fvalue="-3.30" obs_1_distr="53" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="279" model_2_pos_distr="0.00" model_2_neg_distr="355.23" obs_3_distr="43" model_3_pos_distr="0.00" model_3_neg_distr="40.96"/>
+<distribution_point fvalue="-3.10" obs_1_distr="62" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="367" model_2_pos_distr="0.00" model_2_neg_distr="502.62" obs_3_distr="53" model_3_pos_distr="0.01" model_3_neg_distr="72.29"/>
+<distribution_point fvalue="-2.90" obs_1_distr="71" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="464" model_2_pos_distr="0.00" model_2_neg_distr="659.23" obs_3_distr="86" model_3_pos_distr="0.01" model_3_neg_distr="115.15"/>
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+<negmodel_distribution>
+<parameter name="nmc=0" value="0.610"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.390"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="var offset mass diff [massd] (offset: -0.70)">
+<posmodel_distribution>
+<parameter name="massd=0.0" value="0.82"/>
+<parameter name="massd=1.0" value="0.17"/>
+<parameter name="massd=2.0" value="0.01"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="massd=0.0" value="0.49"/>
+<parameter name="massd=1.0" value="0.42"/>
+<parameter name="massd=2.0" value="0.08"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+</mixture_model>
+<mixture_model precursor_ion_charge="2" comments="using training data negative distributions" prior_probability="0.039" est_tot_correct="794.5" tot_num_spectra="20341" num_iterations="36">
+<mixturemodel_distribution name="SEQUEST discrim score [fval]	negmean: -3.23">
+<posmodel_distribution type="gaussian">
+<parameter name="mean" value="5.49"/>
+<parameter name="stdev" value="1.54"/>
+</posmodel_distribution>
+<negmodel_distribution type="gamma">
+<parameter name="m1" value="3.79"/>
+<parameter name="m2" value="16.20"/>
+<parameter name="alpha" value="0.48"/>
+<parameter name="beta" value="7.87"/>
+<parameter name="zero" value="-5.00"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="no. tolerable tryptic term. [ntt]">
+<posmodel_distribution>
+<parameter name="ntt=0" value="0.000"/>
+<parameter name="ntt=1" value="0.006"/>
+<parameter name="ntt=2" value="0.994"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="ntt=0" value="0.000"/>
+<parameter name="ntt=1" value="0.060"/>
+<parameter name="ntt=2" value="0.940"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
+<posmodel_distribution>
+<parameter name="nmc=0" value="0.937"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.063"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="nmc=0" value="0.388"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.612"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="var offset mass diff [massd] (offset: -0.10)">
+<posmodel_distribution>
+<parameter name="massd=-1.0" value="0.08"/>
+<parameter name="massd=0.0" value="0.64"/>
+<parameter name="massd=1.0" value="0.27"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="massd=-1.0" value="0.21"/>
+<parameter name="massd=0.0" value="0.50"/>
+<parameter name="massd=1.0" value="0.28"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+</mixture_model>
+<mixture_model precursor_ion_charge="3" comments="using training data negative distributions" prior_probability="0.019" est_tot_correct="196.9" tot_num_spectra="10427" num_iterations="128">
+<mixturemodel_distribution name="SEQUEST discrim score [fval]	negmean: -2.83">
+<posmodel_distribution type="gaussian">
+<parameter name="mean" value="5.20"/>
+<parameter name="stdev" value="2.23"/>
+</posmodel_distribution>
+<negmodel_distribution type="gamma">
+<parameter name="m1" value="4.49"/>
+<parameter name="m2" value="22.29"/>
+<parameter name="alpha" value="0.46"/>
+<parameter name="beta" value="9.68"/>
+<parameter name="zero" value="-4.93"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="no. tolerable tryptic term. [ntt]">
+<posmodel_distribution>
+<parameter name="ntt=0" value="0.000"/>
+<parameter name="ntt=1" value="0.017"/>
+<parameter name="ntt=2" value="0.983"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="ntt=0" value="0.000"/>
+<parameter name="ntt=1" value="0.065"/>
+<parameter name="ntt=2" value="0.935"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
+<posmodel_distribution>
+<parameter name="nmc=0" value="0.642"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.358"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="nmc=0" value="0.305"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.695"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="var offset mass diff [massd] (offset: 0.60)">
+<posmodel_distribution>
+<parameter name="massd=-2.0" value="0.05"/>
+<parameter name="massd=-1.0" value="0.34"/>
+<parameter name="massd=0.0" value="0.60"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="massd=-2.0" value="0.07"/>
+<parameter name="massd=-1.0" value="0.50"/>
+<parameter name="massd=0.0" value="0.43"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+</mixture_model>
+</peptideprophet_summary>
+<interact_summary time="Wed Jun 14 15:57:55 2006" filename="/var/www/html/isb/interact-4-03-03.xml" directory="/var/www/html/isb" inputfiles="work/john/mult_align/exp/sequest/4-03-03/000.xml work/john/mult_align/exp/sequest/4-03-03/020.xml work/john/mult_align/exp/sequest/4-03-03/040.xml work/john/mult_align/exp/sequest/4-03-03/060.xml work/john/mult_align/exp/sequest/4-03-03/080.xml work/john/mult_align/exp/sequest/4-03-03/100.xml work/john/mult_align/exp/sequest/4-03-03/150.xml work/john/mult_align/exp/sequest/4-03-03/200.xml work/john/mult_align/exp/sequest/4-03-03/300.xml work/john/mult_align/exp/sequest/4-03-03/500.xml work/john/mult_align/exp/sequest/4-03-03/900.xml"/>
+<dataset_derivation generation_no="0"/>
+<msms_run_summary base_name="/work/john/mult_align/exp/sequest/4-03-03/000" search_engine="SEQUEST" database="/work/ms/database/Msmeg_annot.fasta" raw_data_type="mzXML" raw_data=".mzXML" out_data_type="out" out_data=".tgz" sample_enzyme="tryptic">
+<database_refresh_timestamp time="Wed Jun 14 15:59:29 2006" database="/work/ms/database/Msmeg_annot.fasta"/>
+<search_summary base_name="/work/john/mult_align/exp/sequest/4-03-03/000" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="average">
+<enzymatic_search_constraint enzyme="tryptic" max_num_internal_cleavages="2" min_number_termini="2"/>
+<sequence_search_constraint sequence="0"/>
+<sequence_search_constraint sequence="0"/>
+<parameter name="peptide_mass_tol" value="1.000"/>
+<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>
+<peptideprophet_timestamp time="Wed Jun 14 15:59:16 2006"/>
+<search_result spectrum="000.1615.1615.2" start_scan="1615" end_scan="1615" precursor_neutral_mass="2074.2920" assumed_charge="2" index="20">
+<search_hit hit_rank="1" peptide="TNDVAGDGTTTATVLAQALVR" peptide_prev_aa="K" peptide_next_aa="A" protein="MSORF4304" num_tot_proteins="1" num_matched_ions=" 21" tot_num_ions=" 40" calc_neutral_pep_mass="2074.2920" massdiff="+0.0" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mtuberculosis_H37Rv|15610553| groEL1 [Mycobacterium tuberculosis H37Rv]|">
+<search_score name="xcorr" value="4.699"/>
+<search_score name="deltacn" value="0.148"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1070.9"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.8688" all_ntt_prob="(0.0000,0.4043,0.8688)">
+<search_score_summary>
+<parameter name="fval" value="3.8159"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.000"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.1618.1618.2" start_scan="1618" end_scan="1618" precursor_neutral_mass="2075.2920" assumed_charge="2" index="21">
+<search_hit hit_rank="1" peptide="TDDVAGDGTTTATVLAQALVR" peptide_prev_aa="K" peptide_next_aa="E" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 20" tot_num_ions=" 40" calc_neutral_pep_mass="2075.2920" massdiff="+0.0" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="4.647"/>
+<search_score name="deltacn" value="0.634"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1074.5"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9987" all_ntt_prob="(0.0000,0.9877,0.9987)">
+<search_score_summary>
+<parameter name="fval" value="7.3415"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.000"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.1640.1640.3" start_scan="1640" end_scan="1640" precursor_neutral_mass="2075.8920" assumed_charge="3" index="22">
+<search_hit hit_rank="1" peptide="TDDVAGDGTTTATVLAQALVR" peptide_prev_aa="K" peptide_next_aa="E" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 26" tot_num_ions=" 80" calc_neutral_pep_mass="2075.2920" massdiff="+0.6" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="3.379"/>
+<search_score name="deltacn" value="0.383"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="961.3"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.8751" all_ntt_prob="(0.0000,0.6406,0.8751)">
+<search_score_summary>
+<parameter name="fval" value="5.2749"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.600"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.398.398.2" start_scan="398" end_scan="398" precursor_neutral_mass="1414.2920" assumed_charge="2" index="62">
+<search_hit hit_rank="1" peptide="AEIENSDSDYDR" peptide_prev_aa="R" peptide_next_aa="E" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 17" tot_num_ions=" 22" calc_neutral_pep_mass="1413.3920" massdiff="+0.9" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="3.410"/>
+<search_score name="deltacn" value="0.493"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1031.1"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9915" all_ntt_prob="(0.0000,0.9232,0.9915)">
+<search_score_summary>
+<parameter name="fval" value="5.6990"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.900"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.406.406.1" start_scan="406" end_scan="406" precursor_neutral_mass="1413.0920" assumed_charge="1" index="63">
+<search_hit hit_rank="1" peptide="AEIENSDSDYDR" peptide_prev_aa="R" peptide_next_aa="E" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 22" calc_neutral_pep_mass="1413.3920" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="1.489"/>
+<search_score name="deltacn" value="0.339"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="212.7"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.3342" all_ntt_prob="(0.0000,0.0145,0.3342)">
+<search_score_summary>
+<parameter name="fval" value="2.1329"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-0.300"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.414.414.2" start_scan="414" end_scan="414" precursor_neutral_mass="1413.9920" assumed_charge="2" index="64">
+<search_hit hit_rank="1" peptide="AEIENSDSDYDR" peptide_prev_aa="R" peptide_next_aa="E" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 19" tot_num_ions=" 22" calc_neutral_pep_mass="1413.3920" massdiff="+0.6" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="3.690"/>
+<search_score name="deltacn" value="0.480"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1485.6"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9929" all_ntt_prob="(0.0000,0.9349,0.9929)">
+<search_score_summary>
+<parameter name="fval" value="5.8348"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.600"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.523.523.1" start_scan="523" end_scan="523" precursor_neutral_mass="728.5920" assumed_charge="1" index="67">
+<search_hit hit_rank="1" peptide="VLGATPTA" peptide_prev_aa="R" peptide_next_aa="-" protein="MSORF6160" num_tot_proteins="1" num_matched_ions="  8" tot_num_ions=" 14" calc_neutral_pep_mass="728.8920" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0" protein_descr="E: 1e-120  mtuberculosis_H37Rv|15610940| fbpA [Mycobacterium tuberculosis H37Rv]|">
+<search_score name="xcorr" value="1.357"/>
+<search_score name="deltacn" value="0.247"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="176.3"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.0747" all_ntt_prob="(0.0000,0.0024,0.0747)">
+<search_score_summary>
+<parameter name="fval" value="1.6472"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-0.300"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.923.923.2" start_scan="923" end_scan="923" precursor_neutral_mass="1831.6920" assumed_charge="2" index="83">
+<search_hit hit_rank="1" peptide="DETTIVEGAGDAEAIQGR" peptide_prev_aa="K" peptide_next_aa="V" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 20" tot_num_ions=" 34" calc_neutral_pep_mass="1831.8920" massdiff="-0.2" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
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+<search_score name="deltacn" value="0.532"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="945.6"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9953" all_ntt_prob="(0.0000,0.9559,0.9953)">
+<search_score_summary>
+<parameter name="fval" value="5.9794"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-0.200"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="000.927.927.2" start_scan="927" end_scan="927" precursor_neutral_mass="1831.6920" assumed_charge="2" index="85">
+<search_hit hit_rank="1" peptide="DETTIVEGAGDAEAIQGR" peptide_prev_aa="K" peptide_next_aa="V" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 19" tot_num_ions=" 34" calc_neutral_pep_mass="1831.8920" massdiff="-0.2" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="3.884"/>
+<search_score name="deltacn" value="0.583"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="773.2"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9973" all_ntt_prob="(0.0000,0.9743,0.9973)">
+<search_score_summary>
+<parameter name="fval" value="6.4779"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-0.200"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="020.1087.1087.2" start_scan="1087" end_scan="1087" precursor_neutral_mass="1595.5920" assumed_charge="2" index="103">
+<search_hit hit_rank="1" peptide="QIALNGGLEPGVVAEK" peptide_prev_aa="K" peptide_next_aa="V" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 21" tot_num_ions=" 30" calc_neutral_pep_mass="1594.7920" massdiff="+0.8" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="4.000"/>
+<search_score name="deltacn" value="0.642"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1263.0"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9974" all_ntt_prob="(0.0000,0.9748,0.9974)">
+<search_score_summary>
+<parameter name="fval" value="6.9901"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.800"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="020.1092.1092.2" start_scan="1092" end_scan="1092" precursor_neutral_mass="1595.0920" assumed_charge="2" index="105">
+<search_hit hit_rank="1" peptide="QIALNGGLEPGVVAEK" peptide_prev_aa="K" peptide_next_aa="V" protein="MSORF3389" num_tot_proteins="1" num_matched_ions=" 18" tot_num_ions=" 30" calc_neutral_pep_mass="1594.7920" massdiff="+0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|">
+<search_score name="xcorr" value="4.223"/>
+<search_score name="deltacn" value="0.649"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="903.8"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9994" all_ntt_prob="(0.0000,0.9946,0.9994)">
+<search_score_summary>
+<parameter name="fval" value="7.1897"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.300"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="020.1124.1124.2" start_scan="1124" end_scan="1124" precursor_neutral_mass="1863.4919" assumed_charge="2" index="109">
+<search_hit hit_rank="1" peptide="SEESSGGTLASDAQLAALR" peptide_prev_aa="R" peptide_next_aa="E" protein="MSORF2042" num_tot_proteins="1" num_matched_ions=" 21" tot_num_ions=" 36" calc_neutral_pep_mass="1862.9919" massdiff="+0.5" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  mtuberculosis_H37Rv|15608768| rpsA [Mycobacterium tuberculosis H37Rv]|">
+<search_score name="xcorr" value="4.880"/>
+<search_score name="deltacn" value="0.673"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1103.3"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9921" all_ntt_prob="(0.0000,0.9276,0.9921)">
+<search_score_summary>
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+<search_score name="spscore" value="787.8"/>
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+<search_score name="deltacn" value="0.689"/>
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+<search_score name="spscore" value="954.9"/>
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+<parameter name="massd" value="0.500"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="300.1890.1890.2" start_scan="1890" end_scan="1890" precursor_neutral_mass="2591.6921" assumed_charge="2" index="1581">
+<search_hit hit_rank="1" peptide="LVDDNGGVYFVPAFSGLFAPYWR" peptide_prev_aa="R" peptide_next_aa="S" protein="MSORF5691" num_tot_proteins="1" num_matched_ions=" 21" tot_num_ions=" 44" calc_neutral_pep_mass="2590.8921" massdiff="+0.8" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  scoelicolor_A3_2-chr|21219046| glycerol kinase 2 (ATP:glycerol 3-phosphotransferase) (EC 2.7.1.30) [Streptomyces coelicolor A3(2)]|">
+<search_score name="xcorr" value="3.442"/>
+<search_score name="deltacn" value="0.646"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="573.1"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9971" all_ntt_prob="(0.0000,0.9726,0.9971)">
+<search_score_summary>
+<parameter name="fval" value="6.6086"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.800"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="900.1671.1671.3" start_scan="1671" end_scan="1671" precursor_neutral_mass="3494.3921" assumed_charge="3" index="1622">
+<search_hit hit_rank="1" peptide="NVAAGANPIALGSGISKAADAVSEALLASATPVDDKK" peptide_prev_aa="R" peptide_next_aa="A" protein="MSORF4304" num_tot_proteins="1" num_matched_ions=" 21" tot_num_ions="144" calc_neutral_pep_mass="3493.8921" massdiff="+0.5" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="E: 0.0  mtuberculosis_H37Rv|15610553| groEL1 [Mycobacterium tuberculosis H37Rv]|">
+<search_score name="xcorr" value="1.515"/>
+<search_score name="deltacn" value="0.342"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="229.9"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.0522" all_ntt_prob="(0.0000,0.0138,0.0522)">
+<search_score_summary>
+<parameter name="fval" value="2.8408"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="1"/>
+<parameter name="massd" value="0.500"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="900.1907.1907.2" start_scan="1907" end_scan="1907" precursor_neutral_mass="2591.0921" assumed_charge="2" index="1626">
+<search_hit hit_rank="1" peptide="LVDDNGGVYFVPAFSGLFAPYWR" peptide_prev_aa="R" peptide_next_aa="S" protein="MSORF5691" num_tot_proteins="1" num_matched_ions=" 12" tot_num_ions=" 44" calc_neutral_pep_mass="2590.8921" massdiff="+0.2" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="E: 0.0  scoelicolor_A3_2-chr|21219046| glycerol kinase 2 (ATP:glycerol 3-phosphotransferase) (EC 2.7.1.30) [Streptomyces coelicolor A3(2)]|">
+<search_score name="xcorr" value="2.277"/>
+<search_score name="deltacn" value="0.474"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="156.6"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9363" all_ntt_prob="(0.0000,0.6011,0.9363)">
+<search_score_summary>
+<parameter name="fval" value="4.2202"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.200"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>