mspire 0.2.4 → 0.3.0

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Files changed (233) hide show
  1. data/INSTALL +1 -0
  2. data/README +25 -0
  3. data/Rakefile +129 -40
  4. data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
  5. data/bin/bioworks_to_pepxml.rb +1 -0
  6. data/bin/fasta_shaker.rb +1 -96
  7. data/bin/filter_and_validate.rb +5 -0
  8. data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
  9. data/bin/prob_validate.rb +6 -0
  10. data/bin/raw_to_mzXML.rb +2 -2
  11. data/bin/srf_group.rb +1 -0
  12. data/bin/srf_to_sqt.rb +40 -0
  13. data/changelog.txt +68 -0
  14. data/lib/align/chams.rb +6 -6
  15. data/lib/align.rb +4 -3
  16. data/lib/bsearch.rb +120 -0
  17. data/lib/fasta.rb +318 -86
  18. data/lib/group_by.rb +10 -0
  19. data/lib/index_by.rb +11 -0
  20. data/lib/merge_deep.rb +21 -0
  21. data/lib/{spec → ms/converter}/mzxml.rb +77 -109
  22. data/lib/ms/gradient_program.rb +171 -0
  23. data/lib/ms/msrun.rb +209 -0
  24. data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
  25. data/lib/ms/parser/mzdata/axml.rb +12 -0
  26. data/lib/ms/parser/mzdata/dom.rb +160 -0
  27. data/lib/ms/parser/mzdata/libxml.rb +7 -0
  28. data/lib/ms/parser/mzdata.rb +25 -0
  29. data/lib/ms/parser/mzxml/axml.rb +11 -0
  30. data/lib/ms/parser/mzxml/dom.rb +159 -0
  31. data/lib/ms/parser/mzxml/hpricot.rb +253 -0
  32. data/lib/ms/parser/mzxml/libxml.rb +15 -0
  33. data/lib/ms/parser/mzxml/regexp.rb +122 -0
  34. data/lib/ms/parser/mzxml/rexml.rb +72 -0
  35. data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
  36. data/lib/ms/parser/mzxml.rb +175 -0
  37. data/lib/ms/parser.rb +108 -0
  38. data/lib/ms/precursor.rb +10 -0
  39. data/lib/ms/scan.rb +81 -0
  40. data/lib/ms/spectrum.rb +193 -0
  41. data/lib/ms.rb +10 -0
  42. data/lib/mspire.rb +4 -0
  43. data/lib/roc.rb +61 -1
  44. data/lib/sample_enzyme.rb +31 -8
  45. data/lib/scan_i.rb +21 -0
  46. data/lib/spec_id/aa_freqs.rb +7 -3
  47. data/lib/spec_id/bioworks.rb +20 -14
  48. data/lib/spec_id/digestor.rb +139 -0
  49. data/lib/spec_id/mass.rb +116 -0
  50. data/lib/spec_id/parser/proph.rb +236 -0
  51. data/lib/spec_id/precision/filter/cmdline.rb +209 -0
  52. data/lib/spec_id/precision/filter/interactive.rb +134 -0
  53. data/lib/spec_id/precision/filter/output.rb +147 -0
  54. data/lib/spec_id/precision/filter.rb +623 -0
  55. data/lib/spec_id/precision/output.rb +60 -0
  56. data/lib/spec_id/precision/prob/cmdline.rb +139 -0
  57. data/lib/spec_id/precision/prob/output.rb +88 -0
  58. data/lib/spec_id/precision/prob.rb +171 -0
  59. data/lib/spec_id/proph/pep_summary.rb +92 -0
  60. data/lib/spec_id/proph/prot_summary.rb +484 -0
  61. data/lib/spec_id/proph.rb +2 -466
  62. data/lib/spec_id/protein_summary.rb +2 -2
  63. data/lib/spec_id/sequest/params.rb +316 -0
  64. data/lib/spec_id/sequest/pepxml.rb +1513 -0
  65. data/lib/spec_id/sequest.rb +2 -1672
  66. data/lib/spec_id/srf.rb +445 -177
  67. data/lib/spec_id.rb +183 -95
  68. data/lib/spec_id_xml.rb +8 -10
  69. data/lib/transmem/phobius.rb +147 -0
  70. data/lib/transmem/toppred.rb +368 -0
  71. data/lib/transmem.rb +157 -0
  72. data/lib/validator/aa.rb +135 -0
  73. data/lib/validator/background.rb +73 -0
  74. data/lib/validator/bias.rb +95 -0
  75. data/lib/validator/cmdline.rb +260 -0
  76. data/lib/validator/decoy.rb +94 -0
  77. data/lib/validator/digestion_based.rb +69 -0
  78. data/lib/validator/probability.rb +48 -0
  79. data/lib/validator/prot_from_pep.rb +234 -0
  80. data/lib/validator/transmem.rb +272 -0
  81. data/lib/validator/true_pos.rb +46 -0
  82. data/lib/validator.rb +214 -0
  83. data/lib/xml.rb +38 -0
  84. data/lib/xml_style_parser.rb +105 -0
  85. data/lib/xmlparser_wrapper.rb +19 -0
  86. data/script/compile_and_plot_smriti_final.rb +97 -0
  87. data/script/extract_gradient_programs.rb +56 -0
  88. data/script/get_apex_values_rexml.rb +44 -0
  89. data/script/mzXML2timeIndex.rb +1 -1
  90. data/script/smriti_final_analysis.rb +103 -0
  91. data/script/toppred_to_yaml.rb +47 -0
  92. data/script/tpp_installer.rb +1 -1
  93. data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
  94. data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
  95. data/specs/bin/fasta_shaker_spec.rb +259 -0
  96. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
  97. data/specs/bin/filter_and_validate_spec.rb +124 -0
  98. data/specs/bin/ms_to_lmat_spec.rb +34 -0
  99. data/specs/bin/prob_validate_spec.rb +62 -0
  100. data/specs/bin/protein_summary_spec.rb +10 -0
  101. data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
  102. data/specs/gi_spec.rb +22 -0
  103. data/specs/load_bin_path.rb +7 -0
  104. data/specs/merge_deep_spec.rb +13 -0
  105. data/specs/ms/gradient_program_spec.rb +77 -0
  106. data/specs/ms/msrun_spec.rb +455 -0
  107. data/specs/ms/parser_spec.rb +92 -0
  108. data/specs/ms/spectrum_spec.rb +89 -0
  109. data/specs/roc_spec.rb +251 -0
  110. data/specs/rspec_autotest.rb +149 -0
  111. data/specs/sample_enzyme_spec.rb +41 -0
  112. data/specs/spec_helper.rb +133 -0
  113. data/specs/spec_id/aa_freqs_spec.rb +52 -0
  114. data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
  115. data/specs/spec_id/digestor_spec.rb +75 -0
  116. data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
  117. data/specs/spec_id/precision/filter/output_spec.rb +31 -0
  118. data/specs/spec_id/precision/filter_spec.rb +243 -0
  119. data/specs/spec_id/precision/prob_spec.rb +111 -0
  120. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  121. data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
  122. data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
  123. data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
  124. data/specs/spec_id/sequest/params_spec.rb +68 -0
  125. data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
  126. data/specs/spec_id/sqt_spec.rb +138 -0
  127. data/specs/spec_id/srf_spec.rb +209 -0
  128. data/specs/spec_id/srf_spec_helper.rb +302 -0
  129. data/specs/spec_id_helper.rb +33 -0
  130. data/specs/spec_id_spec.rb +361 -0
  131. data/specs/spec_id_xml_spec.rb +33 -0
  132. data/specs/transmem/phobius_spec.rb +423 -0
  133. data/specs/transmem/toppred_spec.rb +297 -0
  134. data/specs/transmem_spec.rb +60 -0
  135. data/specs/transmem_spec_shared.rb +64 -0
  136. data/specs/validator/aa_spec.rb +107 -0
  137. data/specs/validator/background_spec.rb +51 -0
  138. data/specs/validator/bias_spec.rb +146 -0
  139. data/specs/validator/decoy_spec.rb +51 -0
  140. data/specs/validator/fasta_helper.rb +26 -0
  141. data/specs/validator/prot_from_pep_spec.rb +141 -0
  142. data/specs/validator/transmem_spec.rb +145 -0
  143. data/specs/validator/true_pos_spec.rb +58 -0
  144. data/specs/validator_helper.rb +33 -0
  145. data/specs/xml_spec.rb +12 -0
  146. data/test_files/000_pepxml18_small.xml +206 -0
  147. data/test_files/020a.mzXML.timeIndex +4710 -0
  148. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
  149. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
  150. data/test_files/4-03-03_small-prot.xml +321 -0
  151. data/test_files/4-03-03_small.xml +3876 -0
  152. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  153. data/test_files/bioworks-3.3_10prots.xml +5999 -0
  154. data/test_files/bioworks31.params +77 -0
  155. data/test_files/bioworks32.params +62 -0
  156. data/test_files/bioworks33.params +63 -0
  157. data/test_files/bioworks_single_run_small.xml +7237 -0
  158. data/test_files/bioworks_small.fasta +212 -0
  159. data/test_files/bioworks_small.params +63 -0
  160. data/test_files/bioworks_small.phobius +109 -0
  161. data/test_files/bioworks_small.toppred.out +2847 -0
  162. data/test_files/bioworks_small.xml +5610 -0
  163. data/test_files/bioworks_with_INV_small.xml +3753 -0
  164. data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
  165. data/test_files/corrupted_900.srf +0 -0
  166. data/test_files/head_of_7MIX.srf +0 -0
  167. data/test_files/interact-opd1_mods_small-prot.xml +304 -0
  168. data/test_files/messups.fasta +297 -0
  169. data/test_files/opd1/000.my_answer.100lines.xml +101 -0
  170. data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
  171. data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
  172. data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
  173. data/test_files/opd1/000_020-prot.png +0 -0
  174. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
  175. data/test_files/opd1/000_020_3prots-prot.xml +62 -0
  176. data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
  177. data/test_files/opd1/sequest.3.1.params +77 -0
  178. data/test_files/opd1/sequest.3.2.params +62 -0
  179. data/test_files/opd1/twenty_scans.mzXML +418 -0
  180. data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
  181. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  182. data/test_files/opd1/twenty_scans_answ.lmata +9 -0
  183. data/test_files/opd1_020_beginning.RAW +0 -0
  184. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
  185. data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
  186. data/test_files/pepproph_small.xml +4691 -0
  187. data/test_files/phobius.small.noheader.txt +50 -0
  188. data/test_files/phobius.small.small.txt +53 -0
  189. data/test_files/s01_anC1_ld020mM.key.txt +25 -0
  190. data/test_files/s01_anC1_ld020mM.meth +0 -0
  191. data/test_files/small.fasta +297 -0
  192. data/test_files/smallraw.RAW +0 -0
  193. data/test_files/tf_bioworks2excel.bioXML +14340 -0
  194. data/test_files/tf_bioworks2excel.txt.actual +1035 -0
  195. data/test_files/toppred.small.out +416 -0
  196. data/test_files/toppred.xml.out +318 -0
  197. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
  198. data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
  199. data/test_files/yeast_gly_small-prot.xml +265 -0
  200. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
  201. data/test_files/yeast_gly_small.xml +3807 -0
  202. data/test_files/yeast_gly_small2.parentTimes +6 -0
  203. metadata +273 -57
  204. data/bin/filter.rb +0 -6
  205. data/bin/precision.rb +0 -5
  206. data/lib/spec/mzdata/parser.rb +0 -108
  207. data/lib/spec/mzdata.rb +0 -48
  208. data/lib/spec/mzxml/parser.rb +0 -449
  209. data/lib/spec/scan.rb +0 -55
  210. data/lib/spec_id/filter.rb +0 -797
  211. data/lib/spec_id/precision.rb +0 -421
  212. data/lib/toppred.rb +0 -18
  213. data/script/filter-peps.rb +0 -164
  214. data/test/tc_aa_freqs.rb +0 -59
  215. data/test/tc_fasta_shaker.rb +0 -149
  216. data/test/tc_filter.rb +0 -203
  217. data/test/tc_filter_peps.rb +0 -46
  218. data/test/tc_gi.rb +0 -17
  219. data/test/tc_id_class_anal.rb +0 -70
  220. data/test/tc_id_precision.rb +0 -89
  221. data/test/tc_msrun.rb +0 -88
  222. data/test/tc_mzxml.rb +0 -88
  223. data/test/tc_mzxml_to_lmat.rb +0 -36
  224. data/test/tc_peptide_parent_times.rb +0 -27
  225. data/test/tc_precision.rb +0 -60
  226. data/test/tc_roc.rb +0 -166
  227. data/test/tc_sample_enzyme.rb +0 -32
  228. data/test/tc_scan.rb +0 -26
  229. data/test/tc_sequest.rb +0 -336
  230. data/test/tc_spec.rb +0 -78
  231. data/test/tc_spec_id.rb +0 -201
  232. data/test/tc_spec_id_xml.rb +0 -36
  233. data/test/tc_srf.rb +0 -262
data/test_files/yeast_gly_small-prot.xml ADDED
@@ -0,0 +1,265 @@
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+ <?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">
5
+ <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">
6
+ <nsp_information neighboring_bin_smoothing="Y">
7
+ <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"/>
9
+ <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"/>
13
+ <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"/>
15
+ </nsp_information>
16
+ <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" />
18
+ <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" />
21
+ <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" />
22
+ <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" />
23
+ <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>
33
+ <dataset_derivation generation_no="0">
34
+ </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>
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+ <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 ADDED
@@ -0,0 +1,6 @@
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