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/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"/>
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+<parameter name="1&lt;=nmc&lt;=2" value="0.173"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</posmodel_distribution>
+<negmodel_distribution>
+<parameter name="nmc=0" value="0.820"/>
+<parameter name="1&lt;=nmc&lt;=2" value="0.180"/>
+<parameter name="nmc&gt;=3" value="0.000"/>
+</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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+<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>
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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=" 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="sprank" value="1"/>
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+<parameter name="massd" value="0.000"/>
+</search_score_summary>
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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="sprank" value="1"/>
+<peptideprophet_result probability="0.9873" all_ntt_prob="(0.0000,0.9656,0.9873)">
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+<parameter name="massd" value="0.100"/>
+</search_score_summary>
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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="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"/>
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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]">
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+<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>
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+<parameter name="massd" value="-0.100"/>
+</search_score_summary>
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+<search_score name="deltacnstar" value="0"/>
+<search_score name="spscore" value="1586.3"/>
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+<peptideprophet_result probability="0.9987" all_ntt_prob="(0.0000,0.9973,0.9987)">
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+<parameter name="nmc" value="0"/>
+<parameter name="massd" value="-0.300"/>
+</search_score_summary>
+</peptideprophet_result>
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+</search_result>
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+<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>
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+</search_result>
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+<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_score name="deltacn" value="0.170"/>
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+<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=" 21" tot_num_ions=" 30" calc_neutral_pep_mass="1761.9919" massdiff="+0.5" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="Inorganic pyrophosphatase; Ipp1p [Saccharomyces cerevisiae]">
+<search_score name="xcorr" value="5.071"/>
+<search_score name="deltacn" value="0.591"/>
+<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>