RubyGems - mspire - Versions diffs - 0.4.9 → 0.5.0 - Mend

mspire 0.4.9 → 0.5.0

Files changed (255) hide show

data/README +27 -17
data/changelog.txt +31 -62
data/lib/ms/calc.rb +32 -0
data/lib/ms/data/interleaved.rb +60 -0
data/lib/ms/data/lazy_io.rb +73 -0
data/lib/ms/data/lazy_string.rb +15 -0
data/lib/ms/data/simple.rb +59 -0
data/lib/ms/data/transposed.rb +41 -0
data/lib/ms/data.rb +57 -0
data/lib/ms/format/format_error.rb +12 -0
data/lib/ms/spectrum.rb +25 -384
data/lib/ms/support/binary_search.rb +126 -0
data/lib/ms.rb +10 -10
metadata +38 -350
data/INSTALL +0 -58
data/README.rdoc +0 -18
data/Rakefile +0 -330
data/bin/aafreqs.rb +0 -23
data/bin/bioworks2excel.rb +0 -14
data/bin/bioworks_to_pepxml.rb +0 -148
data/bin/bioworks_to_pepxml_gui.rb +0 -225
data/bin/fasta_shaker.rb +0 -5
data/bin/filter_and_validate.rb +0 -5
data/bin/gi2annot.rb +0 -14
data/bin/id_class_anal.rb +0 -112
data/bin/id_precision.rb +0 -172
data/bin/ms_to_lmat.rb +0 -67
data/bin/pepproph_filter.rb +0 -16
data/bin/prob_validate.rb +0 -6
data/bin/protein_summary.rb +0 -6
data/bin/protxml2prots_peps.rb +0 -32
data/bin/raw_to_mzXML.rb +0 -55
data/bin/run_percolator.rb +0 -122
data/bin/sqt_group.rb +0 -26
data/bin/srf_group.rb +0 -27
data/bin/srf_to_sqt.rb +0 -40
data/lib/align/chams.rb +0 -78
data/lib/align.rb +0 -154
data/lib/archive/targz.rb +0 -94
data/lib/bsearch.rb +0 -120
data/lib/core_extensions.rb +0 -16
data/lib/fasta.rb +0 -626
data/lib/gi.rb +0 -124
data/lib/group_by.rb +0 -10
data/lib/index_by.rb +0 -11
data/lib/merge_deep.rb +0 -21
data/lib/ms/converter/mzxml.rb +0 -77
data/lib/ms/gradient_program.rb +0 -170
data/lib/ms/msrun.rb +0 -244
data/lib/ms/msrun_index.rb +0 -108
data/lib/ms/parser/mzdata/axml.rb +0 -67
data/lib/ms/parser/mzdata/dom.rb +0 -175
data/lib/ms/parser/mzdata/libxml.rb +0 -7
data/lib/ms/parser/mzdata.rb +0 -31
data/lib/ms/parser/mzxml/axml.rb +0 -70
data/lib/ms/parser/mzxml/dom.rb +0 -182
data/lib/ms/parser/mzxml/hpricot.rb +0 -253
data/lib/ms/parser/mzxml/libxml.rb +0 -19
data/lib/ms/parser/mzxml/regexp.rb +0 -122
data/lib/ms/parser/mzxml/rexml.rb +0 -72
data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
data/lib/ms/parser/mzxml.rb +0 -282
data/lib/ms/parser.rb +0 -108
data/lib/ms/precursor.rb +0 -25
data/lib/ms/scan.rb +0 -81
data/lib/mspire.rb +0 -4
data/lib/pi_zero.rb +0 -244
data/lib/qvalue.rb +0 -161
data/lib/roc.rb +0 -187
data/lib/sample_enzyme.rb +0 -160
data/lib/scan_i.rb +0 -21
data/lib/spec_id/aa_freqs.rb +0 -170
data/lib/spec_id/bioworks.rb +0 -497
data/lib/spec_id/digestor.rb +0 -138
data/lib/spec_id/mass.rb +0 -179
data/lib/spec_id/parser/proph.rb +0 -335
data/lib/spec_id/precision/filter/cmdline.rb +0 -218
data/lib/spec_id/precision/filter/interactive.rb +0 -134
data/lib/spec_id/precision/filter/output.rb +0 -148
data/lib/spec_id/precision/filter.rb +0 -637
data/lib/spec_id/precision/output.rb +0 -60
data/lib/spec_id/precision/prob/cmdline.rb +0 -160
data/lib/spec_id/precision/prob/output.rb +0 -94
data/lib/spec_id/precision/prob.rb +0 -249
data/lib/spec_id/proph/pep_summary.rb +0 -104
data/lib/spec_id/proph/prot_summary.rb +0 -484
data/lib/spec_id/proph.rb +0 -4
data/lib/spec_id/protein_summary.rb +0 -489
data/lib/spec_id/sequest/params.rb +0 -316
data/lib/spec_id/sequest/pepxml.rb +0 -1458
data/lib/spec_id/sequest.rb +0 -33
data/lib/spec_id/sqt.rb +0 -349
data/lib/spec_id/srf.rb +0 -973
data/lib/spec_id.rb +0 -778
data/lib/spec_id_xml.rb +0 -99
data/lib/transmem/phobius.rb +0 -147
data/lib/transmem/toppred.rb +0 -368
data/lib/transmem.rb +0 -157
data/lib/validator/aa.rb +0 -48
data/lib/validator/aa_est.rb +0 -112
data/lib/validator/background.rb +0 -77
data/lib/validator/bias.rb +0 -95
data/lib/validator/cmdline.rb +0 -431
data/lib/validator/decoy.rb +0 -107
data/lib/validator/digestion_based.rb +0 -70
data/lib/validator/probability.rb +0 -51
data/lib/validator/prot_from_pep.rb +0 -234
data/lib/validator/q_value.rb +0 -32
data/lib/validator/transmem.rb +0 -272
data/lib/validator/true_pos.rb +0 -46
data/lib/validator.rb +0 -197
data/lib/xml.rb +0 -38
data/lib/xml_style_parser.rb +0 -119
data/lib/xmlparser_wrapper.rb +0 -19
data/release_notes.txt +0 -2
data/script/compile_and_plot_smriti_final.rb +0 -97
data/script/create_little_pepxml.rb +0 -61
data/script/degenerate_peptides.rb +0 -47
data/script/estimate_fpr_by_cysteine.rb +0 -226
data/script/extract_gradient_programs.rb +0 -56
data/script/find_cysteine_background.rb +0 -137
data/script/genuine_tps_and_probs.rb +0 -136
data/script/get_apex_values_rexml.rb +0 -44
data/script/histogram_probs.rb +0 -61
data/script/mascot_fix_pepxml.rb +0 -123
data/script/msvis.rb +0 -42
data/script/mzXML2timeIndex.rb +0 -25
data/script/peps_per_bin.rb +0 -67
data/script/prep_dir.rb +0 -121
data/script/simple_protein_digestion.rb +0 -27
data/script/smriti_final_analysis.rb +0 -103
data/script/sqt_to_meta.rb +0 -24
data/script/top_hit_per_scan.rb +0 -67
data/script/toppred_to_yaml.rb +0 -47
data/script/tpp_installer.rb +0 -249
data/specs/align_spec.rb +0 -79
data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
data/specs/bin/fasta_shaker_spec.rb +0 -259
data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
data/specs/bin/filter_and_validate_spec.rb +0 -180
data/specs/bin/ms_to_lmat_spec.rb +0 -34
data/specs/bin/prob_validate_spec.rb +0 -86
data/specs/bin/protein_summary_spec.rb +0 -14
data/specs/fasta_spec.rb +0 -354
data/specs/gi_spec.rb +0 -22
data/specs/load_bin_path.rb +0 -7
data/specs/merge_deep_spec.rb +0 -13
data/specs/ms/gradient_program_spec.rb +0 -77
data/specs/ms/msrun_spec.rb +0 -498
data/specs/ms/parser_spec.rb +0 -92
data/specs/ms/spectrum_spec.rb +0 -87
data/specs/pi_zero_spec.rb +0 -115
data/specs/qvalue_spec.rb +0 -39
data/specs/roc_spec.rb +0 -251
data/specs/rspec_autotest.rb +0 -149
data/specs/sample_enzyme_spec.rb +0 -126
data/specs/spec_helper.rb +0 -135
data/specs/spec_id/aa_freqs_spec.rb +0 -52
data/specs/spec_id/bioworks_spec.rb +0 -148
data/specs/spec_id/digestor_spec.rb +0 -75
data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
data/specs/spec_id/precision/filter/output_spec.rb +0 -31
data/specs/spec_id/precision/filter_spec.rb +0 -246
data/specs/spec_id/precision/prob_spec.rb +0 -44
data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
data/specs/spec_id/protein_summary_spec.rb +0 -189
data/specs/spec_id/sequest/params_spec.rb +0 -68
data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
data/specs/spec_id/sequest_spec.rb +0 -38
data/specs/spec_id/sqt_spec.rb +0 -246
data/specs/spec_id/srf_spec.rb +0 -172
data/specs/spec_id/srf_spec_helper.rb +0 -139
data/specs/spec_id_helper.rb +0 -33
data/specs/spec_id_spec.rb +0 -366
data/specs/spec_id_xml_spec.rb +0 -33
data/specs/transmem/phobius_spec.rb +0 -425
data/specs/transmem/toppred_spec.rb +0 -298
data/specs/transmem_spec.rb +0 -60
data/specs/transmem_spec_shared.rb +0 -64
data/specs/validator/aa_est_spec.rb +0 -66
data/specs/validator/aa_spec.rb +0 -40
data/specs/validator/background_spec.rb +0 -67
data/specs/validator/bias_spec.rb +0 -122
data/specs/validator/decoy_spec.rb +0 -51
data/specs/validator/fasta_helper.rb +0 -26
data/specs/validator/prot_from_pep_spec.rb +0 -141
data/specs/validator/transmem_spec.rb +0 -146
data/specs/validator/true_pos_spec.rb +0 -58
data/specs/validator_helper.rb +0 -33
data/specs/xml_spec.rb +0 -12
data/test_files/000_pepxml18_small.xml +0 -206
data/test_files/020a.mzXML.timeIndex +0 -4710
data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
data/test_files/4-03-03_small-prot.xml +0 -321
data/test_files/4-03-03_small.xml +0 -3876
data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
data/test_files/bioworks-3.3_10prots.xml +0 -5999
data/test_files/bioworks31.params +0 -77
data/test_files/bioworks32.params +0 -62
data/test_files/bioworks33.params +0 -63
data/test_files/bioworks_single_run_small.xml +0 -7237
data/test_files/bioworks_small.fasta +0 -212
data/test_files/bioworks_small.params +0 -63
data/test_files/bioworks_small.phobius +0 -109
data/test_files/bioworks_small.toppred.out +0 -2847
data/test_files/bioworks_small.xml +0 -5610
data/test_files/bioworks_with_INV_small.xml +0 -3753
data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
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 +0 -304
data/test_files/messups.fasta +0 -297
data/test_files/opd1/000.my_answer.100lines.xml +0 -101
data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
data/test_files/opd1/000_020-prot.png +0 -0
data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
data/test_files/opd1/000_020_3prots-prot.xml +0 -62
data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
data/test_files/opd1/sequest.3.1.params +0 -77
data/test_files/opd1/sequest.3.2.params +0 -62
data/test_files/opd1/twenty_scans.mzXML +0 -418
data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
data/test_files/opd1/twenty_scans_answ.lmat +0 -0
data/test_files/opd1/twenty_scans_answ.lmata +0 -9
data/test_files/opd1_020_beginning.RAW +0 -0
data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
data/test_files/pepproph_small.xml +0 -4691
data/test_files/phobius.small.noheader.txt +0 -50
data/test_files/phobius.small.small.txt +0 -53
data/test_files/s01_anC1_ld020mM.key.txt +0 -25
data/test_files/s01_anC1_ld020mM.meth +0 -0
data/test_files/small.fasta +0 -297
data/test_files/small.sqt +0 -87
data/test_files/smallraw.RAW +0 -0
data/test_files/tf_bioworks2excel.bioXML +0 -14340
data/test_files/tf_bioworks2excel.txt.actual +0 -1035
data/test_files/toppred.small.out +0 -416
data/test_files/toppred.xml.out +0 -318
data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
data/test_files/yeast_gly_small-prot.xml +0 -265
data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
data/test_files/yeast_gly_small.xml +0 -3807
data/test_files/yeast_gly_small2.parentTimes +0 -6

data/test_files/yeast_gly_small.xml DELETED Viewed

@@ -1,3807 +0,0 @@
-<?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"/>
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-<parameter name="m1" value="1.37"/>
-<parameter name="m2" value="2.82"/>
-<parameter name="alpha" value="0.68"/>
-<parameter name="beta" value="2.03"/>
-<parameter name="zero" value="-2.00"/>
-<parameter name="minval" value="-2.00"/>
-</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="0.032"/>
-<parameter name="ntt=2" value="0.968"/>
-</posmodel_distribution>
-<negmodel_distribution>
-<parameter name="ntt=0" value="0.000"/>
-<parameter name="ntt=1" value="0.033"/>
-<parameter name="ntt=2" value="0.967"/>
-</negmodel_distribution>
-</mixturemodel_distribution>
-<mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
-<posmodel_distribution>
-<parameter name="nmc=0" value="0.827"/>
-<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"/>
-<search_score name="xcorr" value="1.406"/>
-<search_score name="deltacn" value="0.427"/>
-<search_score name="deltacnstar" value="0"/>
-<search_score name="spscore" value="274.1"/>
-<search_score name="sprank" value="1"/>
-<peptideprophet_result probability="0.3218" all_ntt_prob="(0.0000,0.1939,0.3218)">
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-<parameter name="fval" value="2.6516"/>
-<parameter name="ntt" value="2"/>
-<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]">
-<search_score name="xcorr" value="2.588"/>
-<search_score name="deltacn" value="0.400"/>
-<search_score name="deltacnstar" value="0"/>
-<search_score name="spscore" value="631.0"/>
-<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_result spectrum="005a.1601.1601.3" start_scan="1601" end_scan="1601" precursor_neutral_mass="1596.8920" assumed_charge="3" index="100">
-<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]">
-<search_score name="xcorr" value="3.030"/>
-<search_score name="deltacn" value="0.481"/>
-<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="fval" value="6.3355"/>
-<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>
-<search_result spectrum="005a.1712.1712.2" start_scan="1712" end_scan="1712" precursor_neutral_mass="1263.4919" assumed_charge="2" index="110">
-<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]">
-<search_score name="xcorr" value="2.441"/>
-<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)">
-<search_score_summary>
-<parameter name="fval" value="3.9598"/>
-<parameter name="ntt" value="2"/>
-<parameter name="nmc" value="0"/>
-<parameter name="massd" value="2.000"/>
-</search_score_summary>
-</peptideprophet_result>
-</search_hit>
-</search_result>
-<search_result spectrum="005a.207.207.2" start_scan="207" end_scan="207" precursor_neutral_mass="1356.9919" assumed_charge="2" index="165">
-<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)">
-<search_score_summary>
-<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>
-</search_result>
-<search_result spectrum="005a.4338.4338.2" start_scan="4338" end_scan="4338" precursor_neutral_mass="1213.3919" assumed_charge="2" index="429">
-<search_hit hit_rank="1" peptide="EVIDTILALVK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 16" tot_num_ions=" 20" calc_neutral_pep_mass="1213.4919" massdiff="-0.1" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
-<search_score name="xcorr" value="3.415"/>
-<search_score name="deltacn" value="0.383"/>
-<search_score name="deltacnstar" value="0"/>
-<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)">
-<search_score_summary>
-<parameter name="fval" value="4.9996"/>
-<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="005a.4344.4344.2" start_scan="4344" end_scan="4344" precursor_neutral_mass="1213.1919" assumed_charge="2" index="430">
-<search_hit hit_rank="1" peptide="EVIDTILALVK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 17" tot_num_ions=" 20" calc_neutral_pep_mass="1213.4919" massdiff="-0.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
-<search_score name="xcorr" value="3.507"/>
-<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)">
-<search_score_summary>
-<parameter name="fval" value="5.5625"/>
-<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="005a.4483.4483.2" start_scan="4483" end_scan="4483" precursor_neutral_mass="1212.7919" assumed_charge="2" index="441">
-<search_hit hit_rank="1" peptide="EVIDTILALVK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|6323073|ref|NP_013145.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 20" calc_neutral_pep_mass="1213.4919" massdiff="-0.7" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]">
-<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>
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-<search_score name="deltacn" value="0.572"/>
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-<search_score name="sprank" value="1"/>
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-<parameter name="ntt" value="2"/>
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-<parameter name="massd" value="-1.400"/>
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-<search_hit hit_rank="1" peptide="TTGIVLDSGDGVTHVVPIYAGFSLPHAILR" peptide_prev_aa="R" peptide_next_aa="I" protein="gi|6321069|ref|NP_011147.1|" num_tot_proteins="1" num_matched_ions=" 44" tot_num_ions="116" calc_neutral_pep_mass="3106.5920" massdiff="-0.4" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="Actin; Act1p [Saccharomyces cerevisiae]">
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-<parameter name="massd" value="-1.000"/>
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-<search_hit hit_rank="1" peptide="DDANYIAEFK" peptide_prev_aa="K" peptide_next_aa="N" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 15" tot_num_ions=" 18" calc_neutral_pep_mass="1185.2920" massdiff="+0.4" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-<search_hit hit_rank="1" peptide="DDANYIAEFK" peptide_prev_aa="K" peptide_next_aa="N" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 15" tot_num_ions=" 18" calc_neutral_pep_mass="1185.2920" massdiff="+0.9" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-<search_hit hit_rank="1" peptide="AVDVTALEMVK" peptide_prev_aa="K" peptide_next_aa="W" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 17" tot_num_ions=" 20" calc_neutral_pep_mass="1175.3920" massdiff="-0.7" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-<parameter name="ntt" value="2"/>
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-<parameter name="massd" value="-0.700"/>
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-<search_hit hit_rank="1" peptide="GFFSFATQK" peptide_prev_aa="K" peptide_next_aa="L" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 16" calc_neutral_pep_mass="1032.1920" massdiff="+1.3" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-<search_score name="deltacnstar" value="0"/>
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-<search_hit hit_rank="1" peptide="ITVDELFK" peptide_prev_aa="K" peptide_next_aa="V" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 12" tot_num_ions=" 14" calc_neutral_pep_mass="964.0920" massdiff="+0.1" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-<parameter name="massd" value="0.100"/>
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-<search_hit hit_rank="1" peptide="ITVDELFK" peptide_prev_aa="K" peptide_next_aa="V" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 12" tot_num_ions=" 14" calc_neutral_pep_mass="964.0920" massdiff="+-0.0" num_tol_term="2" num_missed_cleavages="-1" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-<search_hit hit_rank="1" peptide="TQAMQLALALR" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 13" tot_num_ions=" 20" calc_neutral_pep_mass="1215.4919" massdiff="-0.5" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-<search_hit hit_rank="1" peptide="YDLSPIDTLFAMGR" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 16" tot_num_ions=" 26" calc_neutral_pep_mass="1598.7920" massdiff="-0.7" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
-<search_score name="xcorr" value="2.925"/>
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-<search_score name="deltacnstar" value="0"/>
-<search_score name="spscore" value="628.5"/>
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-<parameter name="massd" value="-0.700"/>
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-<search_hit hit_rank="1" peptide="YDLSPIDTLFAMGR" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 18" tot_num_ions=" 26" calc_neutral_pep_mass="1598.7920" massdiff="+1.4" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
-<search_score name="xcorr" value="3.380"/>
-<search_score name="deltacn" value="0.577"/>
-<search_score name="deltacnstar" value="0"/>
-<search_score name="spscore" value="704.1"/>
-<search_score name="sprank" value="1"/>
-<peptideprophet_result probability="0.9970" all_ntt_prob="(0.0000,0.9942,0.9970)">
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-<parameter name="ntt" value="2"/>
-<parameter name="nmc" value="0"/>
-<parameter name="massd" value="1.400"/>
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-<search_hit hit_rank="1" peptide="NYPNHIGLGLFDIHSPR" peptide_prev_aa="K" peptide_next_aa="I" protein="gi|6320936|ref|NP_011015.1|" num_tot_proteins="1" num_matched_ions=" 21" tot_num_ions=" 32" calc_neutral_pep_mass="1950.1920" massdiff="-1.0" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]">
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-</search_result>
-<search_result spectrum="005b.3269.3269.2" start_scan="3269" end_scan="3269" precursor_neutral_mass="1762.4919" assumed_charge="2" index="806">
-<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>