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

mspire 0.2.4 → 0.3.0

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>