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/yeast_gly_small.xml ADDED Viewed

@@ -0,0 +1,3807 @@
+<?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/yeast_gly.xsl"?>
+<?xml-stylesheet type="text/xsl" href="/isb/std_xsl/pepXML_std.xsl"?>
+<msms_pipeline_analysis date="Tue Dec  6 21:02:30 2005" summary_xml="/var/www/html/isb/yeast_gly.xml">
+<peptideprophet_summary version="PeptideProphet v3.0 April 1, 2004" author="AKeller@ISB" inputfiles="/work/john/align/yeast/gly/summary/005a /work/john/align/yeast/gly/summary/005b /work/john/align/yeast/gly/summary/005c /work/john/align/yeast/gly/summary/020a /work/john/align/yeast/gly/summary/020b /work/john/align/yeast/gly/summary/020c /work/john/align/yeast/gly/summary/060a /work/john/align/yeast/gly/summary/060b /work/john/align/yeast/gly/summary/060c /work/john/align/yeast/gly/summary/900a /work/john/align/yeast/gly/summary/900b /work/john/align/yeast/gly/summary/900c" min_prob="0.05" options=" " est_tot_num_correct="2435.7">
+<peptideprophet_timestamp time="Tue Dec  6 21:51:15 2005"/>
+<roc_data_point min_prob="0.99" sensitivity="0.3569" error="0.0027" num_corr="859" num_incorr="2"/>
+<roc_data_point min_prob="0.98" sensitivity="0.4332" error="0.0048" num_corr="1042" num_incorr="5"/>
+<roc_data_point min_prob="0.95" sensitivity="0.5232" error="0.0098" num_corr="1258" num_incorr="13"/>
+<roc_data_point min_prob="0.90" sensitivity="0.5918" error="0.0175" num_corr="1424" num_incorr="25"/>
+<roc_data_point min_prob="0.85" sensitivity="0.6355" error="0.0256" num_corr="1529" num_incorr="40"/>
+<roc_data_point min_prob="0.80" sensitivity="0.6754" error="0.0358" num_corr="1625" num_incorr="60"/>
+<roc_data_point min_prob="0.75" sensitivity="0.7012" error="0.0443" num_corr="1687" num_incorr="78"/>
+<roc_data_point min_prob="0.70" sensitivity="0.7202" error="0.0522" num_corr="1733" num_incorr="95"/>
+<roc_data_point min_prob="0.65" sensitivity="0.7396" error="0.0621" num_corr="1779" num_incorr="118"/>
+<roc_data_point min_prob="0.60" sensitivity="0.7526" error="0.0702" num_corr="1810" num_incorr="137"/>
+<roc_data_point min_prob="0.55" sensitivity="0.7678" error="0.0815" num_corr="1847" num_incorr="164"/>
+<roc_data_point min_prob="0.50" sensitivity="0.7829" error="0.0946" num_corr="1883" num_incorr="197"/>
+<roc_data_point min_prob="0.45" sensitivity="0.8000" error="0.1120" num_corr="1924" num_incorr="243"/>
+<roc_data_point min_prob="0.40" sensitivity="0.8156" error="0.1300" num_corr="1962" num_incorr="293"/>
+<roc_data_point min_prob="0.35" sensitivity="0.8315" error="0.1517" num_corr="2000" num_incorr="358"/>
+<roc_data_point min_prob="0.30" sensitivity="0.8465" error="0.1752" num_corr="2036" num_incorr="433"/>
+<roc_data_point min_prob="0.25" sensitivity="0.8592" error="0.1992" num_corr="2067" num_incorr="514"/>
+<roc_data_point min_prob="0.20" sensitivity="0.8738" error="0.2323" num_corr="2102" num_incorr="636"/>
+<roc_data_point min_prob="0.15" sensitivity="0.8914" error="0.2807" num_corr="2144" num_incorr="837"/>
+<roc_data_point min_prob="0.10" sensitivity="0.9102" error="0.3478" num_corr="2190" num_incorr="1167"/>
+<roc_data_point min_prob="0.05" sensitivity="0.9363" error="0.4697" num_corr="2252" num_incorr="1995"/>
+<roc_data_point min_prob="0.00" sensitivity="1.0000" error="0.9675" num_corr="2406" num_incorr="71643"/>
+<error_point error="0.000" min_prob="1.00" num_corr="2" num_incorr="0"/>
+<error_point error="0.010" min_prob="0.95" num_corr="1264" num_incorr="13"/>
+<error_point error="0.020" min_prob="0.88" num_corr="1462" num_incorr="30"/>
+<error_point error="0.025" min_prob="0.85" num_corr="1524" num_incorr="39"/>
+<error_point error="0.030" min_prob="0.83" num_corr="1575" num_incorr="49"/>
+<error_point error="0.040" min_prob="0.77" num_corr="1658" num_incorr="69"/>
+<error_point error="0.050" min_prob="0.72" num_corr="1721" num_incorr="91"/>
+<error_point error="0.075" min_prob="0.57" num_corr="1827" num_incorr="149"/>
+<error_point error="0.100" min_prob="0.48" num_corr="1897" num_incorr="212"/>
+<distribution_point fvalue="-4.90" obs_1_distr="11" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="3" model_2_pos_distr="0.00" model_2_neg_distr="0.00" obs_3_distr="0" model_3_pos_distr="0.01" 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="11" model_2_pos_distr="0.00" model_2_neg_distr="0.00" obs_3_distr="0" model_3_pos_distr="0.01" model_3_neg_distr="0.00"/>
+<distribution_point fvalue="-4.50" obs_1_distr="22" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="12" model_2_pos_distr="0.00" model_2_neg_distr="0.00" obs_3_distr="1" model_3_pos_distr="0.02" model_3_neg_distr="0.00"/>
+<distribution_point fvalue="-4.30" obs_1_distr="21" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="24" model_2_pos_distr="0.00" model_2_neg_distr="0.04" obs_3_distr="1" model_3_pos_distr="0.03" model_3_neg_distr="0.00"/>
+<distribution_point fvalue="-4.10" obs_1_distr="27" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="39" model_2_pos_distr="0.00" model_2_neg_distr="0.42" obs_3_distr="1" model_3_pos_distr="0.04" model_3_neg_distr="0.01"/>
+<distribution_point fvalue="-3.90" obs_1_distr="39" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="43" model_2_pos_distr="0.00" model_2_neg_distr="2.61" obs_3_distr="8" model_3_pos_distr="0.05" model_3_neg_distr="0.13"/>
+<distribution_point fvalue="-3.70" obs_1_distr="41" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="80" model_2_pos_distr="0.00" model_2_neg_distr="10.94" obs_3_distr="19" model_3_pos_distr="0.07" model_3_neg_distr="1.11"/>
+<distribution_point fvalue="-3.50" obs_1_distr="47" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="102" model_2_pos_distr="0.00" model_2_neg_distr="34.35" obs_3_distr="36" model_3_pos_distr="0.09" model_3_neg_distr="5.60"/>
+<distribution_point fvalue="-3.30" obs_1_distr="43" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="165" model_2_pos_distr="0.00" model_2_neg_distr="86.59" obs_3_distr="40" model_3_pos_distr="0.12" model_3_neg_distr="19.95"/>
+<distribution_point fvalue="-3.10" obs_1_distr="53" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="235" model_2_pos_distr="0.00" model_2_neg_distr="183.86" obs_3_distr="71" model_3_pos_distr="0.16" model_3_neg_distr="54.98"/>
+<distribution_point fvalue="-2.90" obs_1_distr="55" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="318" model_2_pos_distr="0.01" model_2_neg_distr="340.00" obs_3_distr="126" model_3_pos_distr="0.21" model_3_neg_distr="124.67"/>
+<distribution_point fvalue="-2.70" obs_1_distr="61" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="444" model_2_pos_distr="0.01" model_2_neg_distr="561.24" obs_3_distr="189" model_3_pos_distr="0.28" model_3_neg_distr="242.67"/>
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+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="var offset mass diff [massd] (offset: -0.90)">
+<posmodel_distribution>
+<parameter name="massd=-2.0" value="0.11"/>
+<parameter name="massd=-1.0" value="0.16"/>
+<parameter name="massd=0.0" value="0.21"/>
+<parameter name="massd=1.0" value="0.19"/>
+<parameter name="massd=2.0" value="0.20"/>
+<parameter name="massd=3.0" value="0.08"/>
+<parameter name="massd=4.0" value="0.00"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="massd=-2.0" value="0.07"/>
+<parameter name="massd=-1.0" value="0.12"/>
+<parameter name="massd=0.0" value="0.17"/>
+<parameter name="massd=1.0" value="0.19"/>
+<parameter name="massd=2.0" value="0.19"/>
+<parameter name="massd=3.0" value="0.21"/>
+<parameter name="massd=4.0" value="0.05"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+</mixture_model>
+<mixture_model precursor_ion_charge="2" comments="using training data negative distributions" prior_probability="0.037" est_tot_correct="1339.5" tot_num_spectra="36348" num_iterations="42">
+<mixturemodel_distribution name="SEQUEST discrim score [fval]	negmean: -2.97">
+<posmodel_distribution type="gaussian">
+<parameter name="mean" value="4.80"/>
+<parameter name="stdev" value="1.79"/>
+</posmodel_distribution>
+<negmodel_distribution type="gamma">
+<parameter name="m1" value="4.22"/>
+<parameter name="m2" value="19.12"/>
+<parameter name="alpha" value="0.31"/>
+<parameter name="beta" value="13.67"/>
+<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="0.021"/>
+<parameter name="ntt=2" value="0.979"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="ntt=0" value="0.000"/>
+<parameter name="ntt=1" value="0.040"/>
+<parameter name="ntt=2" value="0.960"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
+<posmodel_distribution>
+<parameter name="nmc=0" value="0.966"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.034"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="nmc=0" value="0.532"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.468"/>
+<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="0.01"/>
+<parameter name="massd=-1.0" value="0.10"/>
+<parameter name="massd=0.0" value="0.45"/>
+<parameter name="massd=1.0" value="0.26"/>
+<parameter name="massd=2.0" value="0.10"/>
+<parameter name="massd=3.0" value="0.07"/>
+<parameter name="massd=4.0" value="0.01"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="massd=-2.0" value="0.12"/>
+<parameter name="massd=-1.0" value="0.16"/>
+<parameter name="massd=0.0" value="0.17"/>
+<parameter name="massd=1.0" value="0.18"/>
+<parameter name="massd=2.0" value="0.18"/>
+<parameter name="massd=3.0" value="0.17"/>
+<parameter name="massd=4.0" value="0.03"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+</mixture_model>
+<mixture_model precursor_ion_charge="3" comments="using training data negative distributions" prior_probability="0.030" est_tot_correct="1096.1" tot_num_spectra="36348" num_iterations="54">
+<mixturemodel_distribution name="SEQUEST discrim score [fval]	negmean: -2.58">
+<posmodel_distribution type="gaussian">
+<parameter name="mean" value="4.67"/>
+<parameter name="stdev" value="2.35"/>
+</posmodel_distribution>
+<negmodel_distribution type="gamma">
+<parameter name="m1" value="4.24"/>
+<parameter name="m2" value="19.43"/>
+<parameter name="alpha" value="0.34"/>
+<parameter name="beta" value="12.29"/>
+<parameter name="zero" value="-4.60"/>
+</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="0.015"/>
+<parameter name="ntt=2" value="0.985"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="ntt=0" value="0.000"/>
+<parameter name="ntt=1" value="0.041"/>
+<parameter name="ntt=2" value="0.959"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+<mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
+<posmodel_distribution>
+<parameter name="nmc=0" value="0.734"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.266"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="nmc=0" value="0.329"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.671"/>
+<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=-3.0" value="0.01"/>
+<parameter name="massd=-2.0" value="0.04"/>
+<parameter name="massd=-1.0" value="0.22"/>
+<parameter name="massd=0.0" value="0.42"/>
+<parameter name="massd=1.0" value="0.16"/>
+<parameter name="massd=2.0" value="0.10"/>
+<parameter name="massd=3.0" value="0.05"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="massd=-3.0" value="0.06"/>
+<parameter name="massd=-2.0" value="0.18"/>
+<parameter name="massd=-1.0" value="0.16"/>
+<parameter name="massd=0.0" value="0.17"/>
+<parameter name="massd=1.0" value="0.17"/>
+<parameter name="massd=2.0" value="0.15"/>
+<parameter name="massd=3.0" value="0.11"/>
+</negmodel_distribution>
+</mixturemodel_distribution>
+</mixture_model>
+</peptideprophet_summary>
+<interact_summary time="Tue Dec  6 21:48:31 2005" filename="/var/www/html/isb/yeast_gly.xml" directory="/var/www/html/isb" inputfiles="work/ms/john/align/yeast/gly/summary/005a.xml work/ms/john/align/yeast/gly/summary/005b.xml work/ms/john/align/yeast/gly/summary/005c.xml work/ms/john/align/yeast/gly/summary/020a.xml work/ms/john/align/yeast/gly/summary/020b.xml work/ms/john/align/yeast/gly/summary/020c.xml work/ms/john/align/yeast/gly/summary/060a.xml work/ms/john/align/yeast/gly/summary/060b.xml work/ms/john/align/yeast/gly/summary/060c.xml work/ms/john/align/yeast/gly/summary/900a.xml work/ms/john/align/yeast/gly/summary/900b.xml work/ms/john/align/yeast/gly/summary/900c.xml"/>
+<dataset_derivation generation_no="0"/>
+<msms_run_summary base_name="/work/john/align/yeast/gly/summary/005a" search_engine="SEQUEST" database="/work/ms/database/scerevisiae_all_our.fasta" raw_data_type="mzXML" raw_data=".mzXML" out_data_type="out" out_data=".tgz" sample_enzyme="tryptic">
+<database_refresh_timestamp time="Tue Dec  6 21:51:46 2005" database="/work/ms/database/scerevisiae_all_our.fasta"/>
+<search_summary base_name="/work/john/align/yeast/gly/summary/005a" 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="3.000"/>
+<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="Tue Dec  6 21:51:15 2005"/>
+<search_result spectrum="005a.1163.1163.2" start_scan="1163" end_scan="1163" precursor_neutral_mass="1016.3920" assumed_charge="2" index="28">
+<search_hit hit_rank="1" peptide="LLTTIADAAK" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 15" tot_num_ions=" 18" calc_neutral_pep_mass="1016.1920" massdiff="+0.2" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
+<search_score name="xcorr" value="2.342"/>
+<search_score name="deltacn" value="0.379"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="530.1"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9484" all_ntt_prob="(0.0000,0.9030,0.9484)">
+<search_score_summary>
+<parameter name="fval" value="3.9170"/>
+<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="005a.1243.1243.2" start_scan="1243" end_scan="1243" precursor_neutral_mass="1141.7920" assumed_charge="2" index="37">
+<search_hit hit_rank="1" peptide="YGGVYVGTLSK" peptide_prev_aa="R" peptide_next_aa="P" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="2" num_matched_ions=" 11" tot_num_ions=" 20" calc_neutral_pep_mass="1143.2920" massdiff="-1.5" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
+<alternative_protein protein="gi|6321524|ref|NP_011601.1|" protein_descr="Third, minor isozyme of pyruvate decarboxylase; Pdc6p [Saccharomyces cerevisiae]" num_tol_term="2"/>
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+<search_score name="deltacn" value="0.427"/>
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+<peptideprophet_result probability="0.3218" all_ntt_prob="(0.0000,0.1939,0.3218)">
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+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-1.500"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="005a.1595.1595.3" start_scan="1595" end_scan="1595" precursor_neutral_mass="1596.7920" assumed_charge="3" index="98">
+<search_hit hit_rank="1" peptide="YGGVYVGTLSKPEVK" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 21" tot_num_ions=" 56" calc_neutral_pep_mass="1596.7920" massdiff="+0.0" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
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+<search_score name="deltacn" value="0.400"/>
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+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9016" all_ntt_prob="(0.0000,0.7674,0.9016)">
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+<parameter name="nmc" value="1"/>
+<parameter name="massd" value="0.000"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
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+<search_hit hit_rank="1" peptide="YGGVYVGTLSKPEVK" peptide_prev_aa="R" peptide_next_aa="E" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 29" tot_num_ions=" 56" calc_neutral_pep_mass="1596.7920" massdiff="+0.1" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
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+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1215.9"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9873" all_ntt_prob="(0.0000,0.9656,0.9873)">
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+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="1"/>
+<parameter name="massd" value="0.100"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
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+<search_hit hit_rank="1" peptide="NPVILADACCSR" peptide_prev_aa="K" peptide_next_aa="H" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 15" tot_num_ions=" 22" calc_neutral_pep_mass="1261.4919" massdiff="+2.0" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
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+<search_score name="deltacn" value="0.389"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1077.2"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.8303" all_ntt_prob="(0.0000,0.7126,0.8303)">
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+<parameter name="massd" value="2.000"/>
+</search_score_summary>
+</peptideprophet_result>
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+</search_result>
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+<search_hit hit_rank="1" peptide="NIVEFHSDHMK" peptide_prev_aa="K" peptide_next_aa="I" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 15" tot_num_ions=" 20" calc_neutral_pep_mass="1356.4919" massdiff="+0.5" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
+<search_score name="xcorr" value="2.873"/>
+<search_score name="deltacn" value="0.423"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1010.3"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9896" all_ntt_prob="(0.0000,0.9796,0.9896)">
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+<parameter name="fval" value="4.7723"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.500"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
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+<search_score name="spscore" value="1352.6"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9929" all_ntt_prob="(0.0000,0.9860,0.9929)">
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+<parameter name="massd" value="-0.100"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
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+<search_score name="deltacn" value="0.449"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1586.3"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9987" all_ntt_prob="(0.0000,0.9973,0.9987)">
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+<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>
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+<search_score name="xcorr" value="1.880"/>
+<search_score name="deltacn" value="0.181"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="262.8"/>
+<search_score name="sprank" value="9"/>
+<peptideprophet_result probability="0.0841" all_ntt_prob="(0.0000,0.0444,0.0841)">
+<search_score_summary>
+<parameter name="fval" value="1.2884"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-0.700"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="005a.711.711.2" start_scan="711" end_scan="711" precursor_neutral_mass="996.9920" assumed_charge="2" index="489">
+<search_hit hit_rank="1" peptide="IYEVEGMR" peptide_prev_aa="K" peptide_next_aa="W" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 11" tot_num_ions=" 14" calc_neutral_pep_mass="996.1920" massdiff="+0.8" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
+<search_score name="xcorr" value="2.737"/>
+<search_score name="deltacn" value="0.135"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="726.3"/>
+<search_score name="sprank" value="5"/>
+<peptideprophet_result probability="0.4807" all_ntt_prob="(0.0000,0.3193,0.4807)">
+<search_score_summary>
+<parameter name="fval" value="2.5468"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.800"/>
+</search_score_summary>
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+</search_hit>
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+<search_result spectrum="005a.717.717.2" start_scan="717" end_scan="717" precursor_neutral_mass="995.8920" assumed_charge="2" index="490">
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+<search_score name="xcorr" value="3.102"/>
+<search_score name="deltacn" value="0.170"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="850.7"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9319" all_ntt_prob="(0.0000,0.8740,0.9319)">
+<search_score_summary>
+<parameter name="fval" value="3.5431"/>
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+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1694.0"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.9997" all_ntt_prob="(0.0000,0.9994,0.9997)">
+<search_score_summary>
+<parameter name="fval" value="7.2656"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.500"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="020a.783.783.2" start_scan="783" end_scan="783" precursor_neutral_mass="923.0920" assumed_charge="2" index="1742">
+<search_hit hit_rank="1" peptide="ATNEWFR" peptide_prev_aa="R" peptide_next_aa="I" protein="gi|6319483|ref|NP_009565.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 12" calc_neutral_pep_mass="922.9920" massdiff="+0.1" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0" protein_descr="Inorganic pyrophosphatase; Ipp1p [Saccharomyces cerevisiae]">
+<search_score name="xcorr" value="1.684"/>
+<search_score name="deltacn" value="0.414"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="668.4"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.8512" all_ntt_prob="(0.0000,0.7436,0.8512)">
+<search_score_summary>
+<parameter name="fval" value="3.3678"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="0.100"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="020b.1202.1202.2" start_scan="1202" end_scan="1202" precursor_neutral_mass="1378.1920" assumed_charge="2" index="1791">
+<search_hit hit_rank="1" peptide="VIAIDINDPLAPK" peptide_prev_aa="K" peptide_next_aa="L" protein="gi|6319483|ref|NP_009565.1|" num_tot_proteins="1" num_matched_ions=" 13" tot_num_ions=" 24" calc_neutral_pep_mass="1378.5920" massdiff="-0.4" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="Inorganic pyrophosphatase; Ipp1p [Saccharomyces cerevisiae]">
+<search_score name="xcorr" value="2.296"/>
+<search_score name="deltacn" value="0.444"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="328.4"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.8711" all_ntt_prob="(0.0000,0.7740,0.8711)">
+<search_score_summary>
+<parameter name="fval" value="4.1233"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-0.400"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+<search_result spectrum="060b.3022.3022.2" start_scan="3022" end_scan="3022" precursor_neutral_mass="1764.6919" assumed_charge="2" index="3151">
+<search_hit hit_rank="1" peptide="ALGIMALLDEGETDWK" peptide_prev_aa="K" peptide_next_aa="V" protein="gi|6319483|ref|NP_009565.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 30" calc_neutral_pep_mass="1761.9919" massdiff="+2.7" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="Inorganic pyrophosphatase; Ipp1p [Saccharomyces cerevisiae]">
+<search_score name="xcorr" value="1.528"/>
+<search_score name="deltacn" value="0.331"/>
+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="234.1"/>
+<search_score name="sprank" value="1"/>
+<peptideprophet_result probability="0.0789" all_ntt_prob="(0.0000,0.0416,0.0789)">
+<search_score_summary>
+<parameter name="fval" value="2.0832"/>
+<parameter name="ntt" value="2"/>
+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="2.700"/>
+</search_score_summary>
+</peptideprophet_result>
+</search_hit>
+</search_result>
+</msms_run_summary>
+</msms_pipeline_analysis>