mspire 0.4.9 → 0.5.0

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Files changed (255) hide show
  1. data/README +27 -17
  2. data/changelog.txt +31 -62
  3. data/lib/ms/calc.rb +32 -0
  4. data/lib/ms/data/interleaved.rb +60 -0
  5. data/lib/ms/data/lazy_io.rb +73 -0
  6. data/lib/ms/data/lazy_string.rb +15 -0
  7. data/lib/ms/data/simple.rb +59 -0
  8. data/lib/ms/data/transposed.rb +41 -0
  9. data/lib/ms/data.rb +57 -0
  10. data/lib/ms/format/format_error.rb +12 -0
  11. data/lib/ms/spectrum.rb +25 -384
  12. data/lib/ms/support/binary_search.rb +126 -0
  13. data/lib/ms.rb +10 -10
  14. metadata +38 -350
  15. data/INSTALL +0 -58
  16. data/README.rdoc +0 -18
  17. data/Rakefile +0 -330
  18. data/bin/aafreqs.rb +0 -23
  19. data/bin/bioworks2excel.rb +0 -14
  20. data/bin/bioworks_to_pepxml.rb +0 -148
  21. data/bin/bioworks_to_pepxml_gui.rb +0 -225
  22. data/bin/fasta_shaker.rb +0 -5
  23. data/bin/filter_and_validate.rb +0 -5
  24. data/bin/gi2annot.rb +0 -14
  25. data/bin/id_class_anal.rb +0 -112
  26. data/bin/id_precision.rb +0 -172
  27. data/bin/ms_to_lmat.rb +0 -67
  28. data/bin/pepproph_filter.rb +0 -16
  29. data/bin/prob_validate.rb +0 -6
  30. data/bin/protein_summary.rb +0 -6
  31. data/bin/protxml2prots_peps.rb +0 -32
  32. data/bin/raw_to_mzXML.rb +0 -55
  33. data/bin/run_percolator.rb +0 -122
  34. data/bin/sqt_group.rb +0 -26
  35. data/bin/srf_group.rb +0 -27
  36. data/bin/srf_to_sqt.rb +0 -40
  37. data/lib/align/chams.rb +0 -78
  38. data/lib/align.rb +0 -154
  39. data/lib/archive/targz.rb +0 -94
  40. data/lib/bsearch.rb +0 -120
  41. data/lib/core_extensions.rb +0 -16
  42. data/lib/fasta.rb +0 -626
  43. data/lib/gi.rb +0 -124
  44. data/lib/group_by.rb +0 -10
  45. data/lib/index_by.rb +0 -11
  46. data/lib/merge_deep.rb +0 -21
  47. data/lib/ms/converter/mzxml.rb +0 -77
  48. data/lib/ms/gradient_program.rb +0 -170
  49. data/lib/ms/msrun.rb +0 -244
  50. data/lib/ms/msrun_index.rb +0 -108
  51. data/lib/ms/parser/mzdata/axml.rb +0 -67
  52. data/lib/ms/parser/mzdata/dom.rb +0 -175
  53. data/lib/ms/parser/mzdata/libxml.rb +0 -7
  54. data/lib/ms/parser/mzdata.rb +0 -31
  55. data/lib/ms/parser/mzxml/axml.rb +0 -70
  56. data/lib/ms/parser/mzxml/dom.rb +0 -182
  57. data/lib/ms/parser/mzxml/hpricot.rb +0 -253
  58. data/lib/ms/parser/mzxml/libxml.rb +0 -19
  59. data/lib/ms/parser/mzxml/regexp.rb +0 -122
  60. data/lib/ms/parser/mzxml/rexml.rb +0 -72
  61. data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
  62. data/lib/ms/parser/mzxml.rb +0 -282
  63. data/lib/ms/parser.rb +0 -108
  64. data/lib/ms/precursor.rb +0 -25
  65. data/lib/ms/scan.rb +0 -81
  66. data/lib/mspire.rb +0 -4
  67. data/lib/pi_zero.rb +0 -244
  68. data/lib/qvalue.rb +0 -161
  69. data/lib/roc.rb +0 -187
  70. data/lib/sample_enzyme.rb +0 -160
  71. data/lib/scan_i.rb +0 -21
  72. data/lib/spec_id/aa_freqs.rb +0 -170
  73. data/lib/spec_id/bioworks.rb +0 -497
  74. data/lib/spec_id/digestor.rb +0 -138
  75. data/lib/spec_id/mass.rb +0 -179
  76. data/lib/spec_id/parser/proph.rb +0 -335
  77. data/lib/spec_id/precision/filter/cmdline.rb +0 -218
  78. data/lib/spec_id/precision/filter/interactive.rb +0 -134
  79. data/lib/spec_id/precision/filter/output.rb +0 -148
  80. data/lib/spec_id/precision/filter.rb +0 -637
  81. data/lib/spec_id/precision/output.rb +0 -60
  82. data/lib/spec_id/precision/prob/cmdline.rb +0 -160
  83. data/lib/spec_id/precision/prob/output.rb +0 -94
  84. data/lib/spec_id/precision/prob.rb +0 -249
  85. data/lib/spec_id/proph/pep_summary.rb +0 -104
  86. data/lib/spec_id/proph/prot_summary.rb +0 -484
  87. data/lib/spec_id/proph.rb +0 -4
  88. data/lib/spec_id/protein_summary.rb +0 -489
  89. data/lib/spec_id/sequest/params.rb +0 -316
  90. data/lib/spec_id/sequest/pepxml.rb +0 -1458
  91. data/lib/spec_id/sequest.rb +0 -33
  92. data/lib/spec_id/sqt.rb +0 -349
  93. data/lib/spec_id/srf.rb +0 -973
  94. data/lib/spec_id.rb +0 -778
  95. data/lib/spec_id_xml.rb +0 -99
  96. data/lib/transmem/phobius.rb +0 -147
  97. data/lib/transmem/toppred.rb +0 -368
  98. data/lib/transmem.rb +0 -157
  99. data/lib/validator/aa.rb +0 -48
  100. data/lib/validator/aa_est.rb +0 -112
  101. data/lib/validator/background.rb +0 -77
  102. data/lib/validator/bias.rb +0 -95
  103. data/lib/validator/cmdline.rb +0 -431
  104. data/lib/validator/decoy.rb +0 -107
  105. data/lib/validator/digestion_based.rb +0 -70
  106. data/lib/validator/probability.rb +0 -51
  107. data/lib/validator/prot_from_pep.rb +0 -234
  108. data/lib/validator/q_value.rb +0 -32
  109. data/lib/validator/transmem.rb +0 -272
  110. data/lib/validator/true_pos.rb +0 -46
  111. data/lib/validator.rb +0 -197
  112. data/lib/xml.rb +0 -38
  113. data/lib/xml_style_parser.rb +0 -119
  114. data/lib/xmlparser_wrapper.rb +0 -19
  115. data/release_notes.txt +0 -2
  116. data/script/compile_and_plot_smriti_final.rb +0 -97
  117. data/script/create_little_pepxml.rb +0 -61
  118. data/script/degenerate_peptides.rb +0 -47
  119. data/script/estimate_fpr_by_cysteine.rb +0 -226
  120. data/script/extract_gradient_programs.rb +0 -56
  121. data/script/find_cysteine_background.rb +0 -137
  122. data/script/genuine_tps_and_probs.rb +0 -136
  123. data/script/get_apex_values_rexml.rb +0 -44
  124. data/script/histogram_probs.rb +0 -61
  125. data/script/mascot_fix_pepxml.rb +0 -123
  126. data/script/msvis.rb +0 -42
  127. data/script/mzXML2timeIndex.rb +0 -25
  128. data/script/peps_per_bin.rb +0 -67
  129. data/script/prep_dir.rb +0 -121
  130. data/script/simple_protein_digestion.rb +0 -27
  131. data/script/smriti_final_analysis.rb +0 -103
  132. data/script/sqt_to_meta.rb +0 -24
  133. data/script/top_hit_per_scan.rb +0 -67
  134. data/script/toppred_to_yaml.rb +0 -47
  135. data/script/tpp_installer.rb +0 -249
  136. data/specs/align_spec.rb +0 -79
  137. data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
  138. data/specs/bin/fasta_shaker_spec.rb +0 -259
  139. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
  140. data/specs/bin/filter_and_validate_spec.rb +0 -180
  141. data/specs/bin/ms_to_lmat_spec.rb +0 -34
  142. data/specs/bin/prob_validate_spec.rb +0 -86
  143. data/specs/bin/protein_summary_spec.rb +0 -14
  144. data/specs/fasta_spec.rb +0 -354
  145. data/specs/gi_spec.rb +0 -22
  146. data/specs/load_bin_path.rb +0 -7
  147. data/specs/merge_deep_spec.rb +0 -13
  148. data/specs/ms/gradient_program_spec.rb +0 -77
  149. data/specs/ms/msrun_spec.rb +0 -498
  150. data/specs/ms/parser_spec.rb +0 -92
  151. data/specs/ms/spectrum_spec.rb +0 -87
  152. data/specs/pi_zero_spec.rb +0 -115
  153. data/specs/qvalue_spec.rb +0 -39
  154. data/specs/roc_spec.rb +0 -251
  155. data/specs/rspec_autotest.rb +0 -149
  156. data/specs/sample_enzyme_spec.rb +0 -126
  157. data/specs/spec_helper.rb +0 -135
  158. data/specs/spec_id/aa_freqs_spec.rb +0 -52
  159. data/specs/spec_id/bioworks_spec.rb +0 -148
  160. data/specs/spec_id/digestor_spec.rb +0 -75
  161. data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
  162. data/specs/spec_id/precision/filter/output_spec.rb +0 -31
  163. data/specs/spec_id/precision/filter_spec.rb +0 -246
  164. data/specs/spec_id/precision/prob_spec.rb +0 -44
  165. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  166. data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
  167. data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
  168. data/specs/spec_id/protein_summary_spec.rb +0 -189
  169. data/specs/spec_id/sequest/params_spec.rb +0 -68
  170. data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
  171. data/specs/spec_id/sequest_spec.rb +0 -38
  172. data/specs/spec_id/sqt_spec.rb +0 -246
  173. data/specs/spec_id/srf_spec.rb +0 -172
  174. data/specs/spec_id/srf_spec_helper.rb +0 -139
  175. data/specs/spec_id_helper.rb +0 -33
  176. data/specs/spec_id_spec.rb +0 -366
  177. data/specs/spec_id_xml_spec.rb +0 -33
  178. data/specs/transmem/phobius_spec.rb +0 -425
  179. data/specs/transmem/toppred_spec.rb +0 -298
  180. data/specs/transmem_spec.rb +0 -60
  181. data/specs/transmem_spec_shared.rb +0 -64
  182. data/specs/validator/aa_est_spec.rb +0 -66
  183. data/specs/validator/aa_spec.rb +0 -40
  184. data/specs/validator/background_spec.rb +0 -67
  185. data/specs/validator/bias_spec.rb +0 -122
  186. data/specs/validator/decoy_spec.rb +0 -51
  187. data/specs/validator/fasta_helper.rb +0 -26
  188. data/specs/validator/prot_from_pep_spec.rb +0 -141
  189. data/specs/validator/transmem_spec.rb +0 -146
  190. data/specs/validator/true_pos_spec.rb +0 -58
  191. data/specs/validator_helper.rb +0 -33
  192. data/specs/xml_spec.rb +0 -12
  193. data/test_files/000_pepxml18_small.xml +0 -206
  194. data/test_files/020a.mzXML.timeIndex +0 -4710
  195. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
  196. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
  197. data/test_files/4-03-03_small-prot.xml +0 -321
  198. data/test_files/4-03-03_small.xml +0 -3876
  199. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  200. data/test_files/bioworks-3.3_10prots.xml +0 -5999
  201. data/test_files/bioworks31.params +0 -77
  202. data/test_files/bioworks32.params +0 -62
  203. data/test_files/bioworks33.params +0 -63
  204. data/test_files/bioworks_single_run_small.xml +0 -7237
  205. data/test_files/bioworks_small.fasta +0 -212
  206. data/test_files/bioworks_small.params +0 -63
  207. data/test_files/bioworks_small.phobius +0 -109
  208. data/test_files/bioworks_small.toppred.out +0 -2847
  209. data/test_files/bioworks_small.xml +0 -5610
  210. data/test_files/bioworks_with_INV_small.xml +0 -3753
  211. data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
  212. data/test_files/corrupted_900.srf +0 -0
  213. data/test_files/head_of_7MIX.srf +0 -0
  214. data/test_files/interact-opd1_mods_small-prot.xml +0 -304
  215. data/test_files/messups.fasta +0 -297
  216. data/test_files/opd1/000.my_answer.100lines.xml +0 -101
  217. data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
  218. data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
  219. data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
  220. data/test_files/opd1/000_020-prot.png +0 -0
  221. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
  222. data/test_files/opd1/000_020_3prots-prot.xml +0 -62
  223. data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
  224. data/test_files/opd1/sequest.3.1.params +0 -77
  225. data/test_files/opd1/sequest.3.2.params +0 -62
  226. data/test_files/opd1/twenty_scans.mzXML +0 -418
  227. data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
  228. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  229. data/test_files/opd1/twenty_scans_answ.lmata +0 -9
  230. data/test_files/opd1_020_beginning.RAW +0 -0
  231. data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
  232. data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
  233. data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
  234. data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
  235. data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
  236. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
  237. data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
  238. data/test_files/pepproph_small.xml +0 -4691
  239. data/test_files/phobius.small.noheader.txt +0 -50
  240. data/test_files/phobius.small.small.txt +0 -53
  241. data/test_files/s01_anC1_ld020mM.key.txt +0 -25
  242. data/test_files/s01_anC1_ld020mM.meth +0 -0
  243. data/test_files/small.fasta +0 -297
  244. data/test_files/small.sqt +0 -87
  245. data/test_files/smallraw.RAW +0 -0
  246. data/test_files/tf_bioworks2excel.bioXML +0 -14340
  247. data/test_files/tf_bioworks2excel.txt.actual +0 -1035
  248. data/test_files/toppred.small.out +0 -416
  249. data/test_files/toppred.xml.out +0 -318
  250. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
  251. data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
  252. data/test_files/yeast_gly_small-prot.xml +0 -265
  253. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
  254. data/test_files/yeast_gly_small.xml +0 -3807
  255. data/test_files/yeast_gly_small2.parentTimes +0 -6
data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml DELETED
@@ -1,753 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
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- <?xml-stylesheet type="text/xsl" href="/work/tpp-data/interact-opd1_mods.xsl"?>
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- <msms_pipeline_analysis date="2007-04-24T13:37:08" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd" summary_xml="/work/tpp-data/interact-opd1_mods.xml">
4
- <analysis_summary analysis="database_refresh" time="2007-04-24T13:37:10"/>
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- <analysis_summary analysis="peptideprophet" time="2007-04-24T13:37:09">
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- <peptideprophet_summary version="PeptideProphet v3.0 April 1, 2004 (TPP v2.9 GALE rev.2, Build 200703091101)" author="AKeller@ISB" min_prob="0.05" options=" " est_tot_num_correct="623.8">
7
- <inputfile name="/work/john/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/020"/>
8
- <inputfile name="/work/john/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/040"/>
9
- <roc_data_point min_prob="0.99" sensitivity="0.1070" error="0.0016" num_corr="63" num_incorr="0"/>
10
- <roc_data_point min_prob="0.98" sensitivity="0.1154" error="0.0025" num_corr="68" num_incorr="0"/>
11
- <roc_data_point min_prob="0.95" sensitivity="0.1319" error="0.0064" num_corr="78" num_incorr="0"/>
12
- <roc_data_point min_prob="0.90" sensitivity="0.1760" error="0.0244" num_corr="103" num_incorr="3"/>
13
- <roc_data_point min_prob="0.85" sensitivity="0.2312" error="0.0500" num_corr="136" num_incorr="7"/>
14
- <roc_data_point min_prob="0.80" sensitivity="0.2605" error="0.0666" num_corr="153" num_incorr="11"/>
15
- <roc_data_point min_prob="0.75" sensitivity="0.2934" error="0.0876" num_corr="172" num_incorr="17"/>
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- <roc_data_point min_prob="0.70" sensitivity="0.3342" error="0.1153" num_corr="196" num_incorr="26"/>
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- <roc_data_point min_prob="0.65" sensitivity="0.3870" error="0.1515" num_corr="227" num_incorr="41"/>
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- <roc_data_point min_prob="0.60" sensitivity="0.4561" error="0.1950" num_corr="268" num_incorr="65"/>
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- <roc_data_point min_prob="0.55" sensitivity="0.5004" error="0.2220" num_corr="294" num_incorr="84"/>
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- <roc_data_point min_prob="0.50" sensitivity="0.5440" error="0.2513" num_corr="320" num_incorr="107"/>
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- <roc_data_point min_prob="0.45" sensitivity="0.5885" error="0.2825" num_corr="346" num_incorr="136"/>
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- <roc_data_point min_prob="0.40" sensitivity="0.6306" error="0.3150" num_corr="371" num_incorr="170"/>
23
- <roc_data_point min_prob="0.35" sensitivity="0.6862" error="0.3578" num_corr="403" num_incorr="225"/>
24
- <roc_data_point min_prob="0.30" sensitivity="0.7326" error="0.3953" num_corr="431" num_incorr="281"/>
25
- <roc_data_point min_prob="0.25" sensitivity="0.7787" error="0.4350" num_corr="458" num_incorr="352"/>
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- <roc_data_point min_prob="0.20" sensitivity="0.8284" error="0.4821" num_corr="487" num_incorr="453"/>
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- <roc_data_point min_prob="0.15" sensitivity="0.8621" error="0.5188" num_corr="507" num_incorr="546"/>
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- <roc_data_point min_prob="0.10" sensitivity="0.9117" error="0.5837" num_corr="536" num_incorr="751"/>
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- <roc_data_point min_prob="0.05" sensitivity="0.9552" error="0.6583" num_corr="561" num_incorr="1082"/>
30
- <roc_data_point min_prob="0.00" sensitivity="1.0000" error="0.8753" num_corr="588" num_incorr="4123"/>
31
- <error_point error="0.000" min_prob="1.00" num_corr="42" num_incorr="0"/>
32
- <error_point error="0.010" min_prob="0.94" num_corr="84" num_incorr="1"/>
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- <error_point error="0.020" min_prob="0.92" num_corr="99" num_incorr="2"/>
34
- <error_point error="0.025" min_prob="0.90" num_corr="105" num_incorr="3"/>
35
- <error_point error="0.030" min_prob="0.89" num_corr="111" num_incorr="4"/>
36
- <error_point error="0.040" min_prob="0.87" num_corr="125" num_incorr="5"/>
37
- <error_point error="0.050" min_prob="0.84" num_corr="138" num_incorr="7"/>
38
- <error_point error="0.075" min_prob="0.78" num_corr="163" num_incorr="13"/>
39
- <error_point error="0.100" min_prob="0.73" num_corr="184" num_incorr="21"/>
40
- <distribution_point fvalue="-4.90" obs_1_distr="7" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="14" model_2_pos_distr="0.00" model_2_neg_distr="0.01" obs_3_distr="5" model_3_pos_distr="0.02" model_3_neg_distr="0.00"/>
41
- <distribution_point fvalue="-4.70" obs_1_distr="9" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="22" model_2_pos_distr="0.00" model_2_neg_distr="0.34" obs_3_distr="5" model_3_pos_distr="0.02" model_3_neg_distr="0.00"/>
42
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- <distribution_point fvalue="8.90" obs_1_distr="0" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="0" model_2_pos_distr="0.00" model_2_neg_distr="0.01" obs_3_distr="2" model_3_pos_distr="0.43" model_3_neg_distr="0.01"/>
110
- <distribution_point fvalue="9.10" obs_1_distr="0" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="0" model_2_pos_distr="0.00" model_2_neg_distr="0.01" obs_3_distr="1" model_3_pos_distr="0.34" model_3_neg_distr="0.01"/>
111
- <distribution_point fvalue="9.30" obs_1_distr="0" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="0" model_2_pos_distr="0.00" model_2_neg_distr="0.01" obs_3_distr="0" model_3_pos_distr="0.26" model_3_neg_distr="0.01"/>
112
- <distribution_point fvalue="9.50" obs_1_distr="0" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="0" model_2_pos_distr="0.00" model_2_neg_distr="0.01" obs_3_distr="1" model_3_pos_distr="0.20" model_3_neg_distr="0.01"/>
113
- <distribution_point fvalue="9.70" obs_1_distr="0" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="0" model_2_pos_distr="0.00" model_2_neg_distr="0.01" obs_3_distr="0" model_3_pos_distr="0.15" model_3_neg_distr="0.00"/>
114
- <distribution_point fvalue="9.90" obs_1_distr="0" model_1_pos_distr="0.00" model_1_neg_distr="0.00" obs_2_distr="0" model_2_pos_distr="0.00" model_2_neg_distr="0.00" obs_3_distr="0" model_3_pos_distr="0.11" model_3_neg_distr="0.00"/>
115
- <mixture_model precursor_ion_charge="1" comments="using training data negative distributions" prior_probability="0.004" est_tot_correct="3.8" tot_num_spectra="898" num_iterations="8">
116
- <mixturemodel_distribution name="SEQUEST discrim score [fval] negmean: 1.00">
117
- <posmodel_distribution type="gaussian">
118
- <parameter name="mean" value="2.62"/>
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- <parameter name="stdev" value="0.77"/>
120
- </posmodel_distribution>
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- <negmodel_distribution type="gamma">
122
- <parameter name="m1" value="1.62"/>
123
- <parameter name="m2" value="3.78"/>
124
- <parameter name="alpha" value="0.72"/>
125
- <parameter name="beta" value="2.26"/>
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- <parameter name="zero" value="-2.00"/>
127
- <parameter name="minval" value="-2.00"/>
128
- </negmodel_distribution>
129
- </mixturemodel_distribution>
130
- <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]">
131
- <posmodel_distribution>
132
- <parameter name="ntt=0" value="0.000"/>
133
- <parameter name="ntt=1" value="0.000"/>
134
- <parameter name="ntt=2" value="1.000"/>
135
- </posmodel_distribution>
136
- <negmodel_distribution>
137
- <parameter name="ntt=0" value="0.000"/>
138
- <parameter name="ntt=1" value="0.000"/>
139
- <parameter name="ntt=2" value="1.000"/>
140
- </negmodel_distribution>
141
- </mixturemodel_distribution>
142
- <mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
143
- <posmodel_distribution>
144
- <parameter name="nmc=0" value="0.739"/>
145
- <parameter name="1&lt;=nmc&lt;=2" value="0.261"/>
146
- <parameter name="nmc&gt;=3" value="0.000"/>
147
- </posmodel_distribution>
148
- <negmodel_distribution>
149
- <parameter name="nmc=0" value="0.566"/>
150
- <parameter name="1&lt;=nmc&lt;=2" value="0.434"/>
151
- <parameter name="nmc&gt;=3" value="0.000"/>
152
- </negmodel_distribution>
153
- </mixturemodel_distribution>
154
- <mixturemodel_distribution name="var offset mass diff [massd] (offset: 0.000000)">
155
- <posmodel_distribution>
156
- <parameter name="massd=0.000000" value="1.000000000"/>
157
- </posmodel_distribution>
158
- <negmodel_distribution>
159
- <parameter name="massd=0.000000" value="1.000000000"/>
160
- </negmodel_distribution>
161
- </mixturemodel_distribution>
162
- </mixture_model>
163
- <mixture_model precursor_ion_charge="2" comments="using training data negative distributions" prior_probability="0.115" est_tot_correct="196.3" tot_num_spectra="1706" num_iterations="5">
164
- <mixturemodel_distribution name="SEQUEST discrim score [fval] negmean: -3.25">
165
- <posmodel_distribution type="gaussian">
166
- <parameter name="mean" value="1.89"/>
167
- <parameter name="stdev" value="1.52"/>
168
- </posmodel_distribution>
169
- <negmodel_distribution type="gamma">
170
- <parameter name="m1" value="3.69"/>
171
- <parameter name="m2" value="16.40"/>
172
- <parameter name="alpha" value="0.75"/>
173
- <parameter name="beta" value="4.94"/>
174
- <parameter name="zero" value="-5.00"/>
175
- </negmodel_distribution>
176
- </mixturemodel_distribution>
177
- <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]">
178
- <posmodel_distribution>
179
- <parameter name="ntt=0" value="0.000"/>
180
- <parameter name="ntt=1" value="0.000"/>
181
- <parameter name="ntt=2" value="1.000"/>
182
- </posmodel_distribution>
183
- <negmodel_distribution>
184
- <parameter name="ntt=0" value="0.000"/>
185
- <parameter name="ntt=1" value="0.000"/>
186
- <parameter name="ntt=2" value="1.000"/>
187
- </negmodel_distribution>
188
- </mixturemodel_distribution>
189
- <mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
190
- <posmodel_distribution>
191
- <parameter name="nmc=0" value="0.385"/>
192
- <parameter name="1&lt;=nmc&lt;=2" value="0.615"/>
193
- <parameter name="nmc&gt;=3" value="0.000"/>
194
- </posmodel_distribution>
195
- <negmodel_distribution>
196
- <parameter name="nmc=0" value="0.437"/>
197
- <parameter name="1&lt;=nmc&lt;=2" value="0.563"/>
198
- <parameter name="nmc&gt;=3" value="0.000"/>
199
- </negmodel_distribution>
200
- </mixturemodel_distribution>
201
- <mixturemodel_distribution name="var offset mass diff [massd] (offset: -0.500000)">
202
- <posmodel_distribution>
203
- <parameter name="massd=0.000000" value="0.539533203"/>
204
- <parameter name="massd=1.000000" value="0.460466797"/>
205
- </posmodel_distribution>
206
- <negmodel_distribution>
207
- <parameter name="massd=0.000000" value="0.496137305"/>
208
- <parameter name="massd=1.000000" value="0.503862695"/>
209
- </negmodel_distribution>
210
- </mixturemodel_distribution>
211
- </mixture_model>
212
- <mixture_model precursor_ion_charge="3" comments="using training data negative distributions" prior_probability="0.201" est_tot_correct="423.7" tot_num_spectra="2107" num_iterations="3">
213
- <mixturemodel_distribution name="SEQUEST discrim score [fval] negmean: -2.85">
214
- <posmodel_distribution type="gaussian">
215
- <parameter name="mean" value="3.13"/>
216
- <parameter name="stdev" value="2.15"/>
217
- </posmodel_distribution>
218
- <negmodel_distribution type="gamma">
219
- <parameter name="m1" value="4.44"/>
220
- <parameter name="m2" value="22.22"/>
221
- <parameter name="alpha" value="0.58"/>
222
- <parameter name="beta" value="7.71"/>
223
- <parameter name="zero" value="-5.00"/>
224
- </negmodel_distribution>
225
- </mixturemodel_distribution>
226
- <mixturemodel_distribution name="no. tolerable trypsin term. [ntt]">
227
- <posmodel_distribution>
228
- <parameter name="ntt=0" value="0.000"/>
229
- <parameter name="ntt=1" value="0.000"/>
230
- <parameter name="ntt=2" value="1.000"/>
231
- </posmodel_distribution>
232
- <negmodel_distribution>
233
- <parameter name="ntt=0" value="0.000"/>
234
- <parameter name="ntt=1" value="0.000"/>
235
- <parameter name="ntt=2" value="1.000"/>
236
- </negmodel_distribution>
237
- </mixturemodel_distribution>
238
- <mixturemodel_distribution name="no. missed enz. cleavages [nmc]">
239
- <posmodel_distribution>
240
- <parameter name="nmc=0" value="0.310"/>
241
- <parameter name="1&lt;=nmc&lt;=2" value="0.690"/>
242
- <parameter name="nmc&gt;=3" value="0.000"/>
243
- </posmodel_distribution>
244
- <negmodel_distribution>
245
- <parameter name="nmc=0" value="0.292"/>
246
- <parameter name="1&lt;=nmc&lt;=2" value="0.708"/>
247
- <parameter name="nmc&gt;=3" value="0.000"/>
248
- </negmodel_distribution>
249
- </mixturemodel_distribution>
250
- <mixturemodel_distribution name="var offset mass diff [massd] (offset: 0.000000)">
251
- <posmodel_distribution>
252
- <parameter name="massd=0.000000" value="1.000000000"/>
253
- </posmodel_distribution>
254
- <negmodel_distribution>
255
- <parameter name="massd=0.000000" value="1.000000000"/>
256
- </negmodel_distribution>
257
- </mixturemodel_distribution>
258
- </mixture_model>
259
- </peptideprophet_summary>
260
- </analysis_summary>
261
- <analysis_summary analysis="interact" time="2007-04-24T13:37:06">
262
- <interact_summary filename="/work/tpp-data/interact-opd1_mods.xml" directory="/work/tpp-data">
263
- <inputfile name="sequest/pepxml/020.xml"/>
264
- <inputfile name="sequest/pepxml/040.xml"/>
265
- </interact_summary>
266
- </analysis_summary>
267
- <dataset_derivation generation_no="0"/>
268
- <msms_run_summary base_name="/work/john/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/020" msManufacturer="ThermoFinnigan" msModel="LCQ Deca XP" msIonization="ESI" msMassAnalyzer="Ion Trap" msDetector="UNKNOWN" raw_data_type="raw" raw_data=".mzXML">
269
- <sample_enzyme name="trypsin">
270
- <specificity cut="KR" no_cut="P" sense="C"/>
271
- </sample_enzyme>
272
- <search_summary base_name="/work/john/mspire/test/tfiles_large/opd1_2runs_2mods/sequest/pepxml/020" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="average" out_data_type="out" out_data=".tgz" search_id="1">
273
- <search_database local_path="/project/marcotte/marcotte/ms/database/ecoli_K12_ncbi_20060321.fasta" type="AA"/>
274
- <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/>
275
- <aminoacid_modification binary="N" mass="147.192" symbol="*" massdiff="+15.9994" aminoacid="M" variable="Y"/>
276
- <aminoacid_modification binary="N" mass="167.0581" symbol="#" massdiff="+79.9799" aminoacid="S" variable="Y"/>
277
- <aminoacid_modification binary="N" mass="181.085" symbol="#" massdiff="+79.9799" aminoacid="T" variable="Y"/>
278
- <aminoacid_modification binary="N" mass="243.1559" symbol="#" massdiff="+79.9799" aminoacid="Y" variable="Y"/>
279
- <parameter name="diff_search_options" value="15.999400 M 79.979900 STY 0.000000 M 0.000000 X 0.000000 T 0.000000 Y"/>
280
- <parameter name="digest_mass_range" value="600.0 3500.0"/>
281
- <parameter name="enzyme_info" value="Trypsin(KR/P) 1 1 KR P"/>
282
- <parameter name="first_database_name" value="/project/marcotte/marcotte/ms/database/ecoli_K12_ncbi_20060321.fasta"/>
283
- <parameter name="fragment_ion_tolerance" value="1.0000"/>
284
- <parameter name="fragment_ion_units" value="0"/>
285
- <parameter name="ion_cutoff_percentage" value="0.0000"/>
286
- <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"/>
287
- <parameter name="mass_type_fragment" value="0"/>
288
- <parameter name="mass_type_parent" value="0"/>
289
- <parameter name="match_peak_allowed_error" value="1"/>
290
- <parameter name="match_peak_count" value="0"/>
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- <parameter name="match_peak_tolerance" value="1.0000"/>
292
- <parameter name="max_num_differential_per_peptide" value="3"/>
293
- <parameter name="max_num_internal_cleavage_sites" value="2"/>
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- <parameter name="normalize_xcorr" value="0"/>
295
- <parameter name="nucleotide_reading_frame" value="0"/>
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- <parameter name="num_description_lines" value="5"/>
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- <parameter name="num_output_lines" value="10"/>
298
- <parameter name="num_results" value="250"/>
299
- <parameter name="partial_sequence" value=""/>
300
- <parameter name="peptide_mass_tolerance" value="25.0000"/>
301
- <parameter name="peptide_mass_units" value="2"/>
302
- <parameter name="print_duplicate_references" value="40"/>
303
- <parameter name="protein_mass_filter" value="0 0"/>
304
- <parameter name="remove_precursor_peak" value="0"/>
305
- <parameter name="search_engine" value="SEQUEST"/>
306
- <parameter name="second_database_name" value=""/>
307
- <parameter name="sequence_header_filter" value=""/>
308
- <parameter name="show_fragment_ions" value="0"/>
309
- <parameter name="term_diff_search_options" value="0.000000 0.000000"/>
310
- </search_summary>
311
- <analysis_timestamp analysis="database_refresh" time="2007-04-24T13:37:10" id="1">
312
- <database_refresh_timestamp database="/project/marcotte/marcotte/ms/database/ecoli_K12_ncbi_20060321.fasta"/>
313
- </analysis_timestamp>
314
- <analysis_timestamp analysis="peptideprophet" time="2007-04-24T13:37:09" id="1"/>
315
- <spectrum_query spectrum="020.42.42.3" start_scan="42" end_scan="42" precursor_neutral_mass="1015.77285654469" assumed_charge="3" index="1">
316
- <search_result>
317
- <search_hit hit_rank="1" peptide="GTGVSVTR" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|49176370|ref|YP_026228.1|" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="70" calc_neutral_pep_mass="1015.79382542" massdiff="-0.0209688753124055" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="putative outer membrane protein [Escherichia coli K12]">
318
- <modification_info modified_peptide="GT[181]GVSV[167]TR">
319
- <mod_aminoacid_mass position="2" mass="181.085"/>
320
- <mod_aminoacid_mass position="6" mass="167.0581"/>
321
- <mod_aminoacid_mass position="9" mass="181.085"/>
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- </modification_info>
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- <search_score name="xcorr" value="1.06543827056885"/>
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- <search_score name="deltacn" value="0.192325830459595"/>
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- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="77.8397979736328"/>
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- <search_score name="sprank" value="3"/>
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- <analysis_result analysis="peptideprophet">
329
- <peptideprophet_result probability="0.07881571" all_ntt_prob="(0.0000,0.0000,0.0788)">
330
- <search_score_summary>
331
- <parameter name="fval" value="0.1592"/>
332
- <parameter name="ntt" value="2"/>
333
- <parameter name="nmc" value="0"/>
334
- <parameter name="massd" value="-0.021"/>
335
- </search_score_summary>
336
- </peptideprophet_result>
337
- </analysis_result>
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- </search_hit>
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- </search_result>
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- </spectrum_query>
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- <spectrum_query spectrum="020.58.58.3" start_scan="58" end_scan="58" precursor_neutral_mass="2586.0981739275" assumed_charge="3" index="2">
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- <search_result>
343
- <search_hit hit_rank="1" peptide="AVAAMTRYRQQLLPPLFSALMK" peptide_prev_aa="R" peptide_next_aa="Y" protein="gi|16131943|ref|NP_418541.1|" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="126" calc_neutral_pep_mass="2586.03404942" massdiff="+0.0641245075007646" num_tol_term="2" num_missed_cleavages="2" is_rejected="0" protein_descr="arginine decarboxylase; inducible by acid, catabolic [Escherichia coli K12]">
344
- <modification_info modified_peptide="AVAAMTRYRQQLLPPLFS[167]ALMK">
345
- <mod_aminoacid_mass position="18" mass="167.0581"/>
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- </modification_info>
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- <search_score name="xcorr" value="0.223117798566818"/>
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- <search_score name="deltacn" value="0.644854307174683"/>
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- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="15.7188243865967"/>
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- <search_score name="sprank" value="8"/>
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- <analysis_result analysis="peptideprophet">
353
- <peptideprophet_result probability="0.25764597" all_ntt_prob="(0.0000,0.0000,0.2576)">
354
- <search_score_summary>
355
- <parameter name="fval" value="1.2777"/>
356
- <parameter name="ntt" value="2"/>
357
- <parameter name="nmc" value="1"/>
358
- <parameter name="massd" value="0.064"/>
359
- </search_score_summary>
360
- </peptideprophet_result>
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- </analysis_result>
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- </search_hit>
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- </search_result>
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- </spectrum_query>
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- <spectrum_query spectrum="020.80.80.2" start_scan="80" end_scan="80" precursor_neutral_mass="795.857037471563" assumed_charge="2" index="3">
366
- <search_result>
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- <search_hit hit_rank="1" peptide="YVPPIK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|16129101|ref|NP_415656.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="15" calc_neutral_pep_mass="795.86332542" massdiff="-0.00628794843748892" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="e14 prophage [Escherichia coli K12]">
368
- <modification_info modified_peptide="Y[243]VPPIK">
369
- <mod_aminoacid_mass position="1" mass="243.1559"/>
370
- </modification_info>
371
- <search_score name="xcorr" value="0.705689549446106"/>
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- <search_score name="deltacn" value="0.395860612392426"/>
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- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="152.141448974609"/>
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- <search_score name="sprank" value="1"/>
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- <analysis_result analysis="peptideprophet">
377
- <peptideprophet_result probability="0.11128366" all_ntt_prob="(0.0000,0.0000,0.1113)">
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- <search_score_summary>
379
- <parameter name="fval" value="0.0939"/>
380
- <parameter name="ntt" value="2"/>
381
- <parameter name="nmc" value="0"/>
382
- <parameter name="massd" value="-0.006"/>
383
- </search_score_summary>
384
- </peptideprophet_result>
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- </analysis_result>
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- </search_hit>
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- </spectrum_query>
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- <spectrum_query spectrum="020.104.104.3" start_scan="104" end_scan="104" precursor_neutral_mass="1326.28677256031" assumed_charge="3" index="4">
390
- <search_result>
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- <search_hit hit_rank="1" peptide="LEGEESDLARK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131046|ref|NP_417623.1|" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="60" calc_neutral_pep_mass="1326.30978542" massdiff="-0.0230128596874692" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="hypothetical protein b3154 [Escherichia coli K12]">
392
- <modification_info modified_peptide="LEGEES[167]DLARK">
393
- <mod_aminoacid_mass position="6" mass="167.0581"/>
394
- </modification_info>
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- <search_score name="xcorr" value="0.994660556316376"/>
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- <search_score name="deltacn" value="0.397965431213379"/>
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- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="120.155563354492"/>
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- <search_score name="sprank" value="8"/>
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- <analysis_result analysis="peptideprophet">
401
- <peptideprophet_result probability="0.46972454" all_ntt_prob="(0.0000,0.0000,0.4697)">
402
- <search_score_summary>
403
- <parameter name="fval" value="2.0617"/>
404
- <parameter name="ntt" value="2"/>
405
- <parameter name="nmc" value="1"/>
406
- <parameter name="massd" value="-0.023"/>
407
- </search_score_summary>
408
- </peptideprophet_result>
409
- </analysis_result>
410
- </search_hit>
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- </spectrum_query>
413
- <spectrum_query spectrum="020.158.158.3" start_scan="158" end_scan="158" precursor_neutral_mass="1151.46792490406" assumed_charge="3" index="5">
414
- <search_result>
415
- <search_hit hit_rank="1" peptide="MKDLLKFLK" peptide_prev_aa="-" peptide_next_aa="A" protein="gi|16131818|ref|NP_418415.1|" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="32" calc_neutral_pep_mass="1151.46772442" massdiff="+0.000200484062816031" num_tol_term="2" num_missed_cleavages="2" is_rejected="0" protein_descr="DNA-directed RNA polymerase beta' subunit [Escherichia coli K12]">
416
- <modification_info modified_peptide="M[147]KDLLKFLK">
417
- <mod_aminoacid_mass position="1" mass="147.192"/>
418
- </modification_info>
419
- <search_score name="xcorr" value="0.254981607198715"/>
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- <search_score name="deltacn" value="0.720395803451538"/>
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- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="51.8907661437988"/>
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- <search_score name="sprank" value="1"/>
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- <analysis_result analysis="peptideprophet">
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- <peptideprophet_result probability="0.47041741" all_ntt_prob="(0.0000,0.0000,0.4704)">
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- <parameter name="massd" value="0.000"/>
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- <parameter name="massd" value="0.006"/>
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- <search_hit hit_rank="1" peptide="GLIQLANMLRSQAAR" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|90111091|ref|NP_414689.4|" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="84" calc_neutral_pep_mass="1721.92441442" massdiff="-0.0152053362498918" num_tol_term="2" num_missed_cleavages="1" is_rejected="0" protein_descr="2'-5' RNA ligase [Escherichia coli K12]">
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- <parameter name="nmc" value="1"/>
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- <parameter name="massd" value="-0.015"/>
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- <parameter name="massd" value="-0.011"/>
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- <search_hit hit_rank="1" peptide="VNGGSTQR" peptide_prev_aa="R" peptide_next_aa="K" protein="gi|16129784|ref|NP_416344.1|" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="56" calc_neutral_pep_mass="977.81090142" massdiff="+0.00290971453125621" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="carboxy-terminal protease for penicillin-binding protein 3 [Escherichia coli K12]">
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- <parameter name="massd" value="0.003"/>
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531
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- <search_hit hit_rank="1" peptide="TPVHNTR" peptide_prev_aa="K" peptide_next_aa="-" protein="gi|16130577|ref|NP_417149.1|" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="36" calc_neutral_pep_mass="903.88037542" massdiff="-0.0131585237500076" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="gamma-aminobutyrate transport protein, RpoS-dependent (APC family) [Escherichia coli K12]">
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- <modification_info modified_peptide="T[181]PVHNTR">
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- <parameter name="massd" value="-0.013"/>
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- <search_hit hit_rank="1" peptide="SSSSTNK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|90111655|ref|NP_418298.4|" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="18" calc_neutral_pep_mass="789.68607542" massdiff="+0.0149561921874692" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="putative GTP-binding protein [Escherichia coli K12]">
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- <modification_info modified_peptide="S[167]SSSTNK">
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- <mod_aminoacid_mass position="1" mass="167.0581"/>
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- <peptideprophet_result probability="0.08176422" all_ntt_prob="(0.0000,0.0000,0.0818)">
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- <parameter name="fval" value="-0.0548"/>
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- <parameter name="ntt" value="2"/>
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- <parameter name="massd" value="0.015"/>
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- <search_hit hit_rank="1" peptide="KEDGASKNTSMTSVLK" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|16131714|ref|NP_418310.1|" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="90" calc_neutral_pep_mass="1775.87765042" massdiff="-0.0197108675004074" num_tol_term="2" num_missed_cleavages="2" is_rejected="0" protein_descr="putative resistance protein (transport) [Escherichia coli K12]">
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- <peptideprophet_result probability="0.09169276" all_ntt_prob="(0.0000,0.0000,0.0917)">
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- <parameter name="fval" value="0.2904"/>
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- <parameter name="massd" value="-0.020"/>
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- <search_hit hit_rank="1" peptide="ESDSLEDR" peptide_prev_aa="K" peptide_next_aa="D" protein="gi|16128320|ref|NP_414869.1|" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="42" calc_neutral_pep_mass="1029.89982942" massdiff="-0.0110060784375037" num_tol_term="2" num_missed_cleavages="0" is_rejected="0" protein_descr="putative acetyl-CoA synthetase of the propionate catabolism operon [Escherichia coli K12]">
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- <parameter name="massd" value="-0.011"/>
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- <peptideprophet_result probability="1.00000000" all_ntt_prob="(0.0000,0.0000,1.0000)">
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- <parameter name="massd" value="0.014"/>
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- <modification_info modified_peptide="VAALRVPGGAS[167]LTR">
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- <search_score name="deltacnstar" value="0"/>
737
- <search_score name="spscore" value="118.513412475586"/>
738
- <search_score name="sprank" value="4"/>
739
- <analysis_result analysis="peptideprophet">
740
- <peptideprophet_result probability="0.27738378" all_ntt_prob="(0.0000,0.0000,0.2774)">
741
- <search_score_summary>
742
- <parameter name="fval" value="1.3810"/>
743
- <parameter name="ntt" value="2"/>
744
- <parameter name="nmc" value="1"/>
745
- <parameter name="massd" value="0.021"/>
746
- </search_score_summary>
747
- </peptideprophet_result>
748
- </analysis_result>
749
- </search_hit>
750
- </search_result>
751
- </spectrum_query>
752
- </msms_run_summary>
753
- </msms_pipeline_analysis>