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/yeast_gly_small-prot.xml DELETED
@@ -1,265 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
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- <!DOCTYPE protein_summary SYSTEM "http://localhost/isb-bin/ProteinProphet_v1.9.dtd">
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- <?xml-stylesheet type="text/xsl" href="/isb/yeast_gly-prot.xsl"?>
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- <protein_summary execution_date="Tue Dec 6 21:53:04 2005" program_version="ProteinProphet.pl v2.0 AKeller August 15, 2003">
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- <protein_summary_header reference_database="/work/ms/database/scerevisiae_all_our.fasta" residue_substitution_list="I -> L" enzyme="" occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" source_files="/var/www/html/isb/yeast_gly.xml" source_files_alt="/var/www/html/isb/yeast_gly.xml" output_file="/var/www/html/isb/yeast_gly-prot.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="300.2" run_options="XML_INPUT" num_input_1_spectra="1" num_input_2_spectra="1979" num_input_3_spectra="2266" initial_min_peptide_prob="0.05" initial_peptide_wt_iters="2" nsp_distribution_iters="2" final_peptide_wt_iters="2" total_no_spectrum_ids="2060.4">
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- <nsp_information neighboring_bin_smoothing="Y">
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- <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_excl="0.10" pos_freq="0.095" neg_freq="0.503" pos_to_neg_ratio="0.19"/>
8
- <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.034" neg_freq="0.175" pos_to_neg_ratio="0.20"/>
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- <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.030" neg_freq="0.070" pos_to_neg_ratio="0.43"/>
10
- <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.061" neg_freq="0.059" pos_to_neg_ratio="1.03"/>
11
- <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.091" neg_freq="0.047" pos_to_neg_ratio="1.95"/>
12
- <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.174" neg_freq="0.050" pos_to_neg_ratio="3.47"/>
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- <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.291" neg_freq="0.056" pos_to_neg_ratio="5.20"/>
14
- <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.224" neg_freq="0.040" pos_to_neg_ratio="5.57"/>
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- </nsp_information>
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- <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.818" predicted_num_correct="300" predicted_num_incorrect="1350" />
17
- <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.266" predicted_num_correct="300" predicted_num_incorrect="109" />
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- <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.266" predicted_num_correct="300" predicted_num_incorrect="109" />
19
- <protein_summary_data_filter min_probability="0.30" sensitivity="0.964" false_positive_error_rate="0.203" predicted_num_correct="289" predicted_num_incorrect="74" />
20
- <protein_summary_data_filter min_probability="0.40" sensitivity="0.922" false_positive_error_rate="0.151" predicted_num_correct="277" predicted_num_incorrect="49" />
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- <protein_summary_data_filter min_probability="0.50" sensitivity="0.872" false_positive_error_rate="0.104" predicted_num_correct="262" predicted_num_incorrect="30" />
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- <protein_summary_data_filter min_probability="0.60" sensitivity="0.822" false_positive_error_rate="0.066" predicted_num_correct="247" predicted_num_incorrect="17" />
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- <protein_summary_data_filter min_probability="0.70" sensitivity="0.779" false_positive_error_rate="0.042" predicted_num_correct="234" predicted_num_incorrect="10" />
24
- <protein_summary_data_filter min_probability="0.80" sensitivity="0.727" false_positive_error_rate="0.022" predicted_num_correct="218" predicted_num_incorrect="5" />
25
- <protein_summary_data_filter min_probability="0.90" sensitivity="0.667" false_positive_error_rate="0.010" predicted_num_correct="200" predicted_num_incorrect="2" />
26
- <protein_summary_data_filter min_probability="0.95" sensitivity="0.623" false_positive_error_rate="0.005" predicted_num_correct="187" predicted_num_incorrect="1" />
27
- <protein_summary_data_filter min_probability="0.96" sensitivity="0.617" false_positive_error_rate="0.005" predicted_num_correct="185" predicted_num_incorrect="1" />
28
- <protein_summary_data_filter min_probability="0.97" sensitivity="0.601" false_positive_error_rate="0.004" predicted_num_correct="180" predicted_num_incorrect="1" />
29
- <protein_summary_data_filter min_probability="0.98" sensitivity="0.572" false_positive_error_rate="0.002" predicted_num_correct="172" predicted_num_incorrect="0" />
30
- <protein_summary_data_filter min_probability="0.99" sensitivity="0.536" false_positive_error_rate="0.001" predicted_num_correct="161" predicted_num_incorrect="0" />
31
- <protein_summary_data_filter min_probability="1.00" sensitivity="0.483" false_positive_error_rate="0.000" predicted_num_correct="145" predicted_num_incorrect="0" />
32
- </protein_summary_header>
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- <dataset_derivation generation_no="0">
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- </dataset_derivation><protein_group group_number="1" probability="1.00">
35
- <protein protein_name="gi|6323073|ref|NP_013145.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="48.7" unique_stripped_peptides="MIEIMLPVFDAPQNLVEQAK+NPVILADACCSR+TTYVTQRPVYLGLPANLVDLNVPAK+PVYLGLPANLVDLNVPAK+LIDLTQFPAFVTPMGK+NATFPGVQMK+YGGVYVGTLSK+AQYNEIQGWDHLSLLPTFGAK+LLQTPIDMSLKPNDAESEKEVIDTILALVK+TPANAAVPASTPLK+IYEVEGMR+QVNVNTVFGLPGDFNLSLLDK+YGGVYVGTLSKPEVK+QLLLHHTLGNGDFTVFHR+EVIDTILALVK+MSANISETTAMITDIATAPAEIDR+WAGNANELNAAYAADGYAR+NIVEFHSDHMK+LLTTIADAAK" group_sibling_id="a" total_number_peptides="89" pct_spectrum_ids="3.78">
36
- <annotation protein_description="pyruvate decarboxylase; Pdc1p [Saccharomyces cerevisiae]"/>
37
- <peptide peptide_sequence="QLLLHHTLGNGDFTVFHR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="0.66" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="19.66" n_sibling_peptides_bin="7" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="2105.3921">
38
- <peptide_parent_protein protein_name="gi|6323163|ref|NP_013235.1|"/>
39
- <peptide_parent_protein protein_name="gi|6321524|ref|NP_011601.1|"/>
40
- <peptide_parent_protein protein_name="gi|6320123|ref|NP_010203.1|"/>
41
- </peptide>
42
- <peptide peptide_sequence="TTYVTQRPVYLGLPANLVDLNVPAK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="7" is_contributing_evidence="Y" calc_neutral_pep_mass="2743.1919">
43
- </peptide>
44
- <peptide peptide_sequence="LLQTPIDMSLKPNDAESEKEVIDTILALVK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="3324.8921">
45
- </peptide>
46
- <peptide peptide_sequence="AQYNEIQGWDHLSLLPTFGAK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="8" is_contributing_evidence="Y" calc_neutral_pep_mass="2388.6919">
47
- </peptide>
48
- <peptide peptide_sequence="MIEIMLPVFDAPQNLVEQAK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="6" is_contributing_evidence="Y" calc_neutral_pep_mass="2286.6919">
49
- </peptide>
50
- <peptide peptide_sequence="AQYNEIQGWDHLSLLPTFGAK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2388.6919">
51
- </peptide>
52
- <peptide peptide_sequence="LIDLTQFPAFVTPMGK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="6" is_contributing_evidence="Y" calc_neutral_pep_mass="1778.0920">
53
- </peptide>
54
- <peptide peptide_sequence="PVYLGLPANLVDLNVPAK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="1" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="5" is_contributing_evidence="Y" calc_neutral_pep_mass="1893.1920">
55
- </peptide>
56
- <peptide peptide_sequence="TPANAAVPASTPLK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1337.4919">
57
- </peptide>
58
- <peptide peptide_sequence="WAGNANELNAAYAADGYAR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="0.66" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="19.65" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1998.0920">
59
- <peptide_parent_protein protein_name="gi|6323163|ref|NP_013235.1|"/>
60
- <peptide_parent_protein protein_name="gi|6321524|ref|NP_011601.1|"/>
61
- </peptide>
62
- <peptide peptide_sequence="MSANISETTAMITDIATAPAEIDR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="7" is_contributing_evidence="Y" calc_neutral_pep_mass="2522.7920">
63
- </peptide>
64
- <peptide peptide_sequence="EVIDTILALVK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="6" is_contributing_evidence="Y" calc_neutral_pep_mass="1213.4919">
65
- </peptide>
66
- <peptide peptide_sequence="NIVEFHSDHMK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.56" n_sibling_peptides_bin="7" n_instances="6" is_contributing_evidence="Y" calc_neutral_pep_mass="1356.4919">
67
- </peptide>
68
- <peptide peptide_sequence="QVNVNTVFGLPGDFNLSLLDK" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.57" n_sibling_peptides_bin="7" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="2290.5920">
69
- </peptide>
70
- <peptide peptide_sequence="YGGVYVGTLSKPEVK" charge="3" initial_probability="0.99" nsp_adjusted_probability="1.00" peptide_group_designator="c" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.57" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1596.7920">
71
- </peptide>
72
- <peptide peptide_sequence="TTYVTQRPVYLGLPANLVDLNVPAK" charge="2" initial_probability="0.97" nsp_adjusted_probability="0.99" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.59" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2743.1919">
73
- </peptide>
74
- <peptide peptide_sequence="LLTTIADAAK" charge="2" initial_probability="0.95" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.61" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1016.1920">
75
- </peptide>
76
- <peptide peptide_sequence="NATFPGVQMK" charge="2" initial_probability="0.94" nsp_adjusted_probability="0.99" weight="0.66" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="19.68" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1092.2920">
77
- <peptide_parent_protein protein_name="gi|6323163|ref|NP_013235.1|"/>
78
- </peptide>
79
- <peptide peptide_sequence="YGGVYVGTLSKPEVK" charge="2" initial_probability="0.94" nsp_adjusted_probability="0.99" peptide_group_designator="c" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.61" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1596.7920">
80
- </peptide>
81
- <peptide peptide_sequence="IYEVEGMR" charge="2" initial_probability="0.93" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.62" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="996.1920">
82
- </peptide>
83
- <peptide peptide_sequence="NPVILADACCSR" charge="2" initial_probability="0.83" nsp_adjusted_probability="0.96" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.72" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1261.4919">
84
- </peptide>
85
- <peptide peptide_sequence="YGGVYVGTLSK" charge="2" initial_probability="0.32" nsp_adjusted_probability="0.32" weight="1.00" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="20.24" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1143.2920">
86
- <peptide_parent_protein protein_name="gi|6321524|ref|NP_011601.1|"/>
87
- </peptide>
88
- </protein>
89
- </protein_group>
90
- <protein_group group_number="2" probability="1.00">
91
- <protein protein_name="gi|6324151|ref|NP_014221.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="25.4" unique_stripped_peptides="FADGFLIHSGQPVNDFIDTATR+LVADGVFYAELNEFFTR+YAPGTIVLYAER+INELTLLVQK" group_sibling_id="a" total_number_peptides="8" pct_spectrum_ids="0.33">
92
- <annotation protein_description="Ribosomal protein S3 (rp13) (YS3); Rps3p [Saccharomyces cerevisiae]"/>
93
- <peptide peptide_sequence="FADGFLIHSGQPVNDFIDTATR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.99" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2421.5920">
94
- </peptide>
95
- <peptide peptide_sequence="LVADGVFYAELNEFFTR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.99" n_sibling_peptides_bin="4" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1991.1920">
96
- </peptide>
97
- <peptide peptide_sequence="INELTLLVQK" charge="2" initial_probability="0.99" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.00" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1170.3920">
98
- </peptide>
99
- <peptide peptide_sequence="YAPGTIVLYAER" charge="2" initial_probability="0.06" nsp_adjusted_probability="0.06" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.98" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1352.4919">
100
- </peptide>
101
- </protein>
102
- </protein_group>
103
- <protein_group group_number="3" probability="1.00">
104
- <protein protein_name="gi|6325403|ref|NP_015471.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="19.6" unique_stripped_peptides="YLDGMFAWTLYDAK+LHTAGWTSLHSFAIGLPNAPDLQAAR+AFDTTGEPDAKPYLPEEILWR+AEWGSDIPTTK+YFTPDWLDEK+QKEQFSDGVGYSWIDGLK+IPSTPIDYMAIR" group_sibling_id="a" total_number_peptides="10" pct_spectrum_ids="0.29">
105
- <annotation protein_description="asparagine synthetase; Asn1p [Saccharomyces cerevisiae]"/>
106
- <peptide peptide_sequence="AFDTTGEPDAKPYLPEEILWR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="3.38" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2448.6919">
107
- </peptide>
108
- <peptide peptide_sequence="YLDGMFAWTLYDAK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="3.38" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1693.8920">
109
- </peptide>
110
- <peptide peptide_sequence="IPSTPIDYMAIR" charge="2" initial_probability="0.96" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="3.42" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1376.5920">
111
- </peptide>
112
- <peptide peptide_sequence="AEWGSDIPTTK" charge="2" initial_probability="0.88" nsp_adjusted_probability="0.96" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="3.49" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1204.2920">
113
- </peptide>
114
- <peptide peptide_sequence="YFTPDWLDEK" charge="2" initial_probability="0.30" nsp_adjusted_probability="0.30" weight="0.50" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="4.18" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1313.3920">
115
- <peptide_parent_protein protein_name="gi|6321563|ref|NP_011640.1|"/>
116
- </peptide>
117
- <peptide peptide_sequence="LHTAGWTSLHSFAIGLPNAPDLQAAR" charge="3" initial_probability="0.23" nsp_adjusted_probability="0.23" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="4.15" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2745.0920">
118
- </peptide>
119
- <peptide peptide_sequence="QKEQFSDGVGYSWIDGLK" charge="3" initial_probability="0.12" nsp_adjusted_probability="0.12" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="4.25" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2057.1919">
120
- </peptide>
121
- </protein>
122
- </protein_group>
123
- <protein_group group_number="4" probability="1.00">
124
- <protein protein_name="gi|6320801|ref|NP_010880.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="60.5" unique_stripped_peptides="LEDLSPSTHNMEVPVVK+NEYQLLDIDDGFLSLMNMDGDTK+KLEDLSPSTHNMEVPVVK+RNEYQLLDIDDGFLSLMNMDGDTK+VHLVAIDIFTGK+DLMVTIISAMGEEAAISFK+NEYQLLDIDDGFLSLMNMDGDTKDDVK+APEGELGDSLQTAFDEGK" group_sibling_id="a" total_number_peptides="14" pct_spectrum_ids="0.63">
125
- <annotation protein_description="Translation initiation factor eIF-5A; Hyp2p [Saccharomyces cerevisiae]"/>
126
- <peptide peptide_sequence="APEGELGDSLQTAFDEGK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.59" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1863.8920">
127
- </peptide>
128
- <peptide peptide_sequence="VHLVAIDIFTGK" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.59" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1312.5920">
129
- </peptide>
130
- <peptide peptide_sequence="KLEDLSPSTHNMEVPVVK" charge="3" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.59" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2023.2920">
131
- </peptide>
132
- <peptide peptide_sequence="NEYQLLDIDDGFLSLMNMDGDTKDDVK" charge="3" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.59" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="3105.3921">
133
- </peptide>
134
- <peptide peptide_sequence="RNEYQLLDIDDGFLSLMNMDGDTK" charge="3" initial_probability="0.98" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.61" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2804.0920">
135
- </peptide>
136
- <peptide peptide_sequence="DLMVTIISAMGEEAAISFK" charge="3" initial_probability="0.96" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="6.65" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="2026.3920">
137
- <peptide_parent_protein protein_name="gi|6322507|ref|NP_012581.1|"/>
138
- </peptide>
139
- <peptide peptide_sequence="NEYQLLDIDDGFLSLMNMDGDTK" charge="2" initial_probability="0.86" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.73" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2647.8921">
140
- </peptide>
141
- <peptide peptide_sequence="LEDLSPSTHNMEVPVVK" charge="3" initial_probability="0.85" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.74" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1895.1920">
142
- </peptide>
143
- </protein>
144
- </protein_group>
145
- <protein_group group_number="5" probability="1.00">
146
- <protein protein_name="gi|6319725|ref|NP_009807.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="11.4" unique_stripped_peptides="LILPGVGNYGHFVDNLFNR+IPVIASSGAGVPEHFEEAFLK+IPALEVASLYFR+AGLNVIENFLK" group_sibling_id="a" total_number_peptides="5" pct_spectrum_ids="0.24">
147
- <annotation protein_description="glutamine amidotransferase:cyclase, also called imidazole glycerol phosphate synthase; His7p [Saccharomyces cerevisiae]"/>
148
- <peptide peptide_sequence="IPALEVASLYFR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.83" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1378.5920">
149
- </peptide>
150
- <peptide peptide_sequence="LILPGVGNYGHFVDNLFNR" charge="3" initial_probability="0.97" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.86" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2145.3921">
151
- </peptide>
152
- <peptide peptide_sequence="AGLNVIENFLK" charge="2" initial_probability="0.97" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.86" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1217.3920">
153
- </peptide>
154
- <peptide peptide_sequence="IPVIASSGAGVPEHFEEAFLK" charge="3" initial_probability="0.90" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.93" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2198.4919">
155
- </peptide>
156
- </protein>
157
- </protein_group>
158
- <protein_group group_number="6" probability="1.00">
159
- <protein protein_name="gi|6321069|ref|NP_011147.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="28.0" unique_stripped_peptides="GYSFSTTAER+AVFPSIVGR+YPIEHGIVTNWDDMEK+TTGIVLDSGDGVTHVVPIYAGFSLPHAILR+IWHHTFYNELR+VAPEEHPVLLTEAPMNPK+HQGIMVGMGQK" group_sibling_id="a" total_number_peptides="14" pct_spectrum_ids="0.60">
160
- <annotation protein_description="Actin; Act1p [Saccharomyces cerevisiae]"/>
161
- <peptide peptide_sequence="TTGIVLDSGDGVTHVVPIYAGFSLPHAILR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.47" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="3106.5920">
162
- </peptide>
163
- <peptide peptide_sequence="YPIEHGIVTNWDDMEK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.47" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1947.0920">
164
- </peptide>
165
- <peptide peptide_sequence="HQGIMVGMGQK" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.47" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1185.3920">
166
- </peptide>
167
- <peptide peptide_sequence="GYSFSTTAER" charge="2" initial_probability="0.96" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.51" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1118.1920">
168
- </peptide>
169
- <peptide peptide_sequence="VAPEEHPVLLTEAPMNPK" charge="2" initial_probability="0.94" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.53" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1972.2920">
170
- </peptide>
171
- <peptide peptide_sequence="AVFPSIVGR" charge="2" initial_probability="0.89" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.57" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="945.0920">
172
- </peptide>
173
- <peptide peptide_sequence="IWHHTFYNELR" charge="3" initial_probability="0.68" nsp_adjusted_probability="0.92" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.79" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1515.6920">
174
- </peptide>
175
- </protein>
176
- </protein_group>
177
- <protein_group group_number="7" probability="1.00">
178
- <protein protein_name="gi|6320936|ref|NP_011015.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="32.5" unique_stripped_peptides="DDANYIAEFK+PVLLGPVSYLFLGK+QTLSVGIVDGR+AVDVTALEMVK+TQAMQLALALRDEVNDLEAAGIK+VIQVDEPALR+SAYYTWAAEAFR+VFNLPLFPTTTIGSFPQTK+NYPNHIGLGLFDIHSPR+ITVDELFK+GLPVAALHVDFVR+VVVATSSSLLHTPVDLNNETK+TQAMQLALALR+ADKDSLDLEPLSLLEQLLPLYTEILSK+WFDSNYHYVR+GFFSFATQK+YVRPPIIVGDLSR+YDLSPIDTLFAMGR+YVRPPIIVGDLSRPK+WFDSNYHYVRPTFSK" group_sibling_id="a" total_number_peptides="59" pct_spectrum_ids="2.63">
179
- <annotation protein_description="vitamin B12-(cobalamin)-independent isozyme of methionine synthase (also called N5-methyltetrahydrofolate homocysteine methyltransferase or 5-methyltetrahydropteroyl triglutamate homocysteine methyltransferase); Met6p [Saccharomyces cerevisiae]"/>
180
- <peptide peptide_sequence="NYPNHIGLGLFDIHSPR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1950.1920">
181
- </peptide>
182
- <peptide peptide_sequence="VVVATSSSLLHTPVDLNNETK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="2224.4919">
183
- </peptide>
184
- <peptide peptide_sequence="TQAMQLALALRDEVNDLEAAGIK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2470.7920">
185
- </peptide>
186
- <peptide peptide_sequence="YDLSPIDTLFAMGR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="5" is_contributing_evidence="Y" calc_neutral_pep_mass="1598.7920">
187
- </peptide>
188
- <peptide peptide_sequence="SAYYTWAAEAFR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1435.5920">
189
- </peptide>
190
- <peptide peptide_sequence="GLPVAALHVDFVR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1393.5920">
191
- </peptide>
192
- <peptide peptide_sequence="PVLLGPVSYLFLGK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="1" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="11" is_contributing_evidence="Y" calc_neutral_pep_mass="1502.8920">
193
- </peptide>
194
- <peptide peptide_sequence="NYPNHIGLGLFDIHSPR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1950.1920">
195
- </peptide>
196
- <peptide peptide_sequence="VFNLPLFPTTTIGSFPQTK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="5" is_contributing_evidence="Y" calc_neutral_pep_mass="2108.4919">
197
- </peptide>
198
- <peptide peptide_sequence="AVDVTALEMVK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1175.3920">
199
- </peptide>
200
- <peptide peptide_sequence="DDANYIAEFK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1185.2920">
201
- </peptide>
202
- <peptide peptide_sequence="YVRPPIIVGDLSR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="5" is_contributing_evidence="Y" calc_neutral_pep_mass="1484.7920">
203
- </peptide>
204
- <peptide peptide_sequence="ADKDSLDLEPLSLLEQLLPLYTEILSK" charge="3" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.17" n_sibling_peptides_bin="7" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="3057.4919">
205
- </peptide>
206
- <peptide peptide_sequence="ITVDELFK" charge="2" initial_probability="0.98" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.18" n_sibling_peptides_bin="7" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="964.0920">
207
- </peptide>
208
- <peptide peptide_sequence="TQAMQLALALR" charge="2" initial_probability="0.95" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.22" n_sibling_peptides_bin="7" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1215.4919">
209
- </peptide>
210
- <peptide peptide_sequence="QTLSVGIVDGR" charge="2" initial_probability="0.70" nsp_adjusted_probability="0.93" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.46" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1144.2920">
211
- </peptide>
212
- <peptide peptide_sequence="WFDSNYHYVRPTFSK" charge="3" initial_probability="0.57" nsp_adjusted_probability="0.87" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.59" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1947.0920">
213
- </peptide>
214
- <peptide peptide_sequence="YVRPPIIVGDLSRPK" charge="3" initial_probability="0.49" nsp_adjusted_probability="0.79" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.68" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1709.9919">
215
- </peptide>
216
- <peptide peptide_sequence="GFFSFATQK" charge="2" initial_probability="0.27" nsp_adjusted_probability="0.27" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="16.89" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1032.1920">
217
- </peptide>
218
- <peptide peptide_sequence="WFDSNYHYVR" charge="3" initial_probability="0.12" nsp_adjusted_probability="0.12" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="17.05" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1386.4919">
219
- </peptide>
220
- <peptide peptide_sequence="VIQVDEPALR" charge="2" initial_probability="0.10" nsp_adjusted_probability="0.10" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="17.06" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1139.2920">
221
- </peptide>
222
- </protein>
223
- </protein_group>
224
- <protein_group group_number="8" probability="1.00">
225
- <protein protein_name="gi|6319809|ref|NP_009890.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="12.8" unique_stripped_peptides="NILVDLHSQGLLLQQYR+VSGMFLGEVLR+ETELSLLQSLR+IPDDLLDDENVTSDDLFGFLAR+SKIPDDLLDDENVTSDDLFGFLARR" group_sibling_id="a" total_number_peptides="5" pct_spectrum_ids="0.20">
226
- <annotation protein_description="Glucokinase; Glk1p [Saccharomyces cerevisiae]"/>
227
- <peptide peptide_sequence="VSGMFLGEVLR" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.18" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1207.4919">
228
- </peptide>
229
- <peptide peptide_sequence="NILVDLHSQGLLLQQYR" charge="3" initial_probability="0.97" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.19" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2010.2920">
230
- </peptide>
231
- <peptide peptide_sequence="ETELSLLQSLR" charge="2" initial_probability="0.85" nsp_adjusted_probability="0.95" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.32" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1288.4919">
232
- </peptide>
233
- <peptide peptide_sequence="SKIPDDLLDDENVTSDDLFGFLARR" charge="3" initial_probability="0.36" nsp_adjusted_probability="0.27" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.81" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2852.0920">
234
- </peptide>
235
- <peptide peptide_sequence="IPDDLLDDENVTSDDLFGFLAR" charge="2" initial_probability="0.07" nsp_adjusted_probability="0.07" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="3.16" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2480.6919">
236
- </peptide>
237
- </protein>
238
- </protein_group>
239
- <protein_group group_number="9" probability="1.00">
240
- <protein protein_name="gi|6319483|ref|NP_009565.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="12.5" unique_stripped_peptides="ATNEWFR+ALGIMALLDEGETDWK+VIAIDINDPLAPK" group_sibling_id="a" total_number_peptides="4" pct_spectrum_ids="0.14">
241
- <annotation protein_description="Inorganic pyrophosphatase; Ipp1p [Saccharomyces cerevisiae]"/>
242
- <peptide peptide_sequence="ALGIMALLDEGETDWK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.72" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1761.9919">
243
- </peptide>
244
- <peptide peptide_sequence="VIAIDINDPLAPK" charge="2" initial_probability="0.87" nsp_adjusted_probability="0.93" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.85" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1378.5920">
245
- </peptide>
246
- <peptide peptide_sequence="ATNEWFR" charge="2" initial_probability="0.85" nsp_adjusted_probability="0.92" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.87" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="922.9920">
247
- </peptide>
248
- </protein>
249
- </protein_group>
250
- <protein_group group_number="10" probability="1.00">
251
- <protein protein_name="gi|6320362|ref|NP_010442.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="20.8" unique_stripped_peptides="EDPLLDFK+QTIHVLEQPDRPQPR+FILLLANHPHFELK+IAGVLGATGSVGQR+PGFIICISNCSTAGLVAPLKPLIEK" group_sibling_id="a" total_number_peptides="6" pct_spectrum_ids="0.19">
252
- <annotation protein_description="aspartic beta semi-aldehyde dehydrogenase; Hom2p [Saccharomyces cerevisiae]"/>
253
- <peptide peptide_sequence="IAGVLGATGSVGQR" charge="2" initial_probability="0.95" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.33" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1285.4919">
254
- </peptide>
255
- <peptide peptide_sequence="QTIHVLEQPDRPQPR" charge="3" initial_probability="0.51" nsp_adjusted_probability="0.67" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.77" n_sibling_peptides_bin="4" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1813.9919">
256
- </peptide>
257
- <peptide peptide_sequence="EDPLLDFK" charge="2" initial_probability="0.50" nsp_adjusted_probability="0.66" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.78" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="976.0920">
258
- </peptide>
259
- <peptide peptide_sequence="FILLLANHPHFELK" charge="3" initial_probability="0.18" nsp_adjusted_probability="0.18" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.10" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1691.9919">
260
- </peptide>
261
- <peptide peptide_sequence="PGFIICISNCSTAGLVAPLKPLIEK" charge="3" initial_probability="0.15" nsp_adjusted_probability="0.15" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="1" n_sibling_peptides="2.13" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2585.1919">
262
- </peptide>
263
- </protein>
264
- </protein_group>
265
- </protein_summary>
data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes DELETED
@@ -1,6 +0,0 @@
1
- # PROTCUTOFF: 1.0 NSPPEPCUTOFF: 1.0 INITPEPCUTOFF: 1.0
2
- # These are the times of the precursor scan!
3
- # filename sequence charge time1 prec_mz prec_int time2 ...
4
- 020a EVIDTILALVK 2 5545.870000 609.063965 4030201.000000 5537.900000 607.687988 9531986.000000
5
- 020a TPANAAVPASTPLK 2 1037.230000 669.406616 6435475.000000 1029.090000 669.593262 5464264.000000
6
- 020a YVRPPIIVGDLSR 3 2769.160000 495.767334 3464513.000000 2759.730000 495.924683 2817155.000000