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/4-03-03_small-prot.xml DELETED
@@ -1,321 +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/interact-4-03-03-prot.xsl"?>
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- <protein_summary execution_date="Wed Jun 14 15:59:40 2006" program_version="ProteinProphet.pl v2.0 AKeller August 15, 2003">
5
- <protein_summary_header reference_database="/work/ms/database/Msmeg_annot.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/interact-4-03-03.xml" source_files_alt="/var/www/html/isb/interact-4-03-03.xml" output_file="/var/www/html/isb/interact-4-03-03-prot.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="200.9" run_options="XML_INPUT" num_input_1_spectra="146" num_input_2_spectra="1032" num_input_3_spectra="462" initial_min_peptide_prob="0.05" initial_peptide_wt_iters="2" nsp_distribution_iters="2" final_peptide_wt_iters="1" total_no_spectrum_ids="1010.1">
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="0.098" neg_freq="0.557" pos_to_neg_ratio="0.18"/>
8
- <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.026" neg_freq="0.128" pos_to_neg_ratio="0.21"/>
9
- <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.028" neg_freq="0.018" pos_to_neg_ratio="1.51"/>
10
- <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.093" neg_freq="0.034" pos_to_neg_ratio="2.78"/>
11
- <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.155" neg_freq="0.054" pos_to_neg_ratio="2.89"/>
12
- <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.252" neg_freq="0.084" pos_to_neg_ratio="2.99"/>
13
- <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.251" neg_freq="0.091" pos_to_neg_ratio="2.77" alt_pos_to_neg_ratio="2.99"/>
14
- <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.096" neg_freq="0.034" pos_to_neg_ratio="2.81" alt_pos_to_neg_ratio="2.99"/>
15
- </nsp_information>
16
- <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.686" predicted_num_correct="201" predicted_num_incorrect="439" />
17
- <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.115" predicted_num_correct="201" predicted_num_incorrect="26" />
18
- <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.115" predicted_num_correct="201" predicted_num_incorrect="26" />
19
- <protein_summary_data_filter min_probability="0.30" sensitivity="0.981" false_positive_error_rate="0.070" predicted_num_correct="197" predicted_num_incorrect="15" />
20
- <protein_summary_data_filter min_probability="0.40" sensitivity="0.973" false_positive_error_rate="0.056" predicted_num_correct="195" predicted_num_incorrect="12" />
21
- <protein_summary_data_filter min_probability="0.50" sensitivity="0.962" false_positive_error_rate="0.043" predicted_num_correct="193" predicted_num_incorrect="9" />
22
- <protein_summary_data_filter min_probability="0.60" sensitivity="0.946" false_positive_error_rate="0.031" predicted_num_correct="190" predicted_num_incorrect="6" />
23
- <protein_summary_data_filter min_probability="0.70" sensitivity="0.933" false_positive_error_rate="0.024" predicted_num_correct="187" predicted_num_incorrect="5" />
24
- <protein_summary_data_filter min_probability="0.80" sensitivity="0.906" false_positive_error_rate="0.016" predicted_num_correct="182" predicted_num_incorrect="3" />
25
- <protein_summary_data_filter min_probability="0.90" sensitivity="0.864" false_positive_error_rate="0.008" predicted_num_correct="174" predicted_num_incorrect="1" />
26
- <protein_summary_data_filter min_probability="0.95" sensitivity="0.823" false_positive_error_rate="0.004" predicted_num_correct="165" predicted_num_incorrect="1" />
27
- <protein_summary_data_filter min_probability="0.96" sensitivity="0.813" false_positive_error_rate="0.004" predicted_num_correct="163" predicted_num_incorrect="1" />
28
- <protein_summary_data_filter min_probability="0.97" sensitivity="0.789" false_positive_error_rate="0.003" predicted_num_correct="159" predicted_num_incorrect="0" />
29
- <protein_summary_data_filter min_probability="0.98" sensitivity="0.765" false_positive_error_rate="0.002" predicted_num_correct="154" predicted_num_incorrect="0" />
30
- <protein_summary_data_filter min_probability="0.99" sensitivity="0.731" false_positive_error_rate="0.001" predicted_num_correct="147" predicted_num_incorrect="0" />
31
- <protein_summary_data_filter min_probability="1.00" sensitivity="0.657" false_positive_error_rate="0.000" predicted_num_correct="132" 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="MSORF4131" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="17.0" unique_stripped_peptides="TSHITVIVESRPPK+WAPQAASEPVAK" group_sibling_id="a" total_number_peptides="10" pct_spectrum_ids="0.81">
36
- <annotation protein_description="E: 2e-45 mleprae|15827997| 50S ribosomal protein L22 [Mycobacterium leprae]|"/>
37
- <peptide peptide_sequence="WAPQAASEPVAK" 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="1.83" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1254.3920">
38
- </peptide>
39
- <peptide peptide_sequence="TSHITVIVESRPPK" charge="2" initial_probability="0.93" nsp_adjusted_probability="0.98" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.87" n_sibling_peptides_bin="4" n_instances="6" is_contributing_evidence="Y" calc_neutral_pep_mass="1563.7920">
40
- </peptide>
41
- <peptide peptide_sequence="TSHITVIVESRPPK" charge="3" initial_probability="0.90" nsp_adjusted_probability="0.96" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.90" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1563.7920">
42
- </peptide>
43
- </protein>
44
- </protein_group>
45
- <protein_group group_number="2" probability="1.00">
46
- <protein protein_name="MSORF6160" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="23.6" unique_stripped_peptides="VEFQSGGPGAPALYLLDGMR+WETFLTQELPAWLAANR+ANDPTENVATIANNGTR+VLGATPTA+PGLPVEYLEVPSAAMGR" group_sibling_id="a" total_number_peptides="8" pct_spectrum_ids="0.79">
47
- <annotation protein_description="E: 1e-120 mtuberculosis_H37Rv|15610940| fbpA [Mycobacterium tuberculosis H37Rv]|"/>
48
- <peptide peptide_sequence="ANDPTENVATIANNGTR" 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="2.91" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1757.7920">
49
- </peptide>
50
- <peptide peptide_sequence="WETFLTQELPAWLAANR" 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="2.91" n_sibling_peptides_bin="5" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="2046.2920">
51
- </peptide>
52
- <peptide peptide_sequence="VEFQSGGPGAPALYLLDGMR" charge="2" initial_probability="0.98" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.92" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2078.3921">
53
- </peptide>
54
- <peptide peptide_sequence="PGLPVEYLEVPSAAMGR" charge="2" initial_probability="0.92" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="1" n_sibling_peptides="2.98" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1786.0920">
55
- </peptide>
56
- <peptide peptide_sequence="VLGATPTA" charge="1" initial_probability="0.07" nsp_adjusted_probability="0.07" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="3.91" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="728.8920">
57
- </peptide>
58
- </protein>
59
- </protein_group>
60
- <protein_group group_number="3" probability="1.00">
61
- <protein protein_name="MSORF4075" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="40.9" unique_stripped_peptides="GITINISHVEYQTDKR+TTLTAAITK+FPDLNESR+AFDQIDNAPEER+GQVVVKPGTTTPHTEFEGQVYILSK+HYAHVDAPGHADYIK+EHVLLARQVGVPYILVALNK+LLDQGQAGDNVGLLLR+ELLAAQDFDEEAPVVR+GITINISHVEYQTDK+GVINVNEEVEIVGIRPETTK+VLHDKFPDLNESR" group_sibling_id="a" total_number_peptides="28" pct_spectrum_ids="2.54">
62
- <annotation protein_description="E: 0.0 mtuberculosis_H37Rv|15607825| tuf [Mycobacterium tuberculosis H37Rv]|"/>
63
- <peptide peptide_sequence="GQVVVKPGTTTPHTEFEGQVYILSK" 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="10.21" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2716.0920">
64
- </peptide>
65
- <peptide peptide_sequence="GVINVNEEVEIVGIRPETTK" 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="10.21" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2196.4919">
66
- </peptide>
67
- <peptide peptide_sequence="LLDQGQAGDNVGLLLR" 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="10.21" n_sibling_peptides_bin="6" n_instances="7" is_contributing_evidence="Y" calc_neutral_pep_mass="1681.8920">
68
- </peptide>
69
- <peptide peptide_sequence="GITINISHVEYQTDK" 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="10.21" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1717.8920">
70
- </peptide>
71
- <peptide peptide_sequence="AFDQIDNAPEER" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.22" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1404.4919">
72
- </peptide>
73
- <peptide peptide_sequence="ELLAAQDFDEEAPVVR" 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="10.22" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1801.9919">
74
- </peptide>
75
- <peptide peptide_sequence="VLHDKFPDLNESR" charge="2" initial_probability="0.95" nsp_adjusted_probability="0.98" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.26" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1569.6920">
76
- </peptide>
77
- <peptide peptide_sequence="AFDQIDNAPEER" charge="1" initial_probability="0.93" nsp_adjusted_probability="0.98" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.28" n_sibling_peptides_bin="6" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1404.4919">
78
- </peptide>
79
- <peptide peptide_sequence="TTLTAAITK" charge="2" initial_probability="0.93" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.28" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="919.0920">
80
- </peptide>
81
- <peptide peptide_sequence="GITINISHVEYQTDKR" charge="2" initial_probability="0.89" nsp_adjusted_probability="0.96" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.32" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1874.0920">
82
- </peptide>
83
- <peptide peptide_sequence="FPDLNESR" charge="1" initial_probability="0.74" nsp_adjusted_probability="0.90" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.47" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="976.9920">
84
- </peptide>
85
- <peptide peptide_sequence="VLHDKFPDLNESR" charge="3" initial_probability="0.55" nsp_adjusted_probability="0.78" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.66" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1569.6920">
86
- </peptide>
87
- <peptide peptide_sequence="HYAHVDAPGHADYIK" charge="2" initial_probability="0.15" nsp_adjusted_probability="0.15" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="11.06" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1693.7920">
88
- </peptide>
89
- <peptide peptide_sequence="EHVLLARQVGVPYILVALNK" 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="11.11" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2232.6919">
90
- </peptide>
91
- </protein>
92
- </protein_group>
93
- <protein_group group_number="4" probability="1.00">
94
- <protein protein_name="MSORF2454" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="17.2" unique_stripped_peptides="AEAEDLLK+IITSPSFGGDR+VVALSGGYSR+QVLSHGLVPIIEPEVTISIADK" group_sibling_id="a" total_number_peptides="4" pct_spectrum_ids="0.36">
95
- <annotation protein_description="E: 4e-94 fnucleatum_nucleatum_ATCC25586|19703667| Fructose-bisphosphate aldolase [Fusobacterium nucleatum subsp. nucleatum ATCC 25586]|"/>
96
- <peptide peptide_sequence="VVALSGGYSR" charge="2" initial_probability="0.93" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.21" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1008.1920">
97
- </peptide>
98
- <peptide peptide_sequence="QVLSHGLVPIIEPEVTISIADK" charge="2" initial_probability="0.89" nsp_adjusted_probability="0.96" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.26" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2358.7920">
99
- </peptide>
100
- <peptide peptide_sequence="AEAEDLLK" charge="1" initial_probability="0.85" nsp_adjusted_probability="0.94" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.30" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="887.9920">
101
- </peptide>
102
- <peptide peptide_sequence="IITSPSFGGDR" charge="2" initial_probability="0.48" nsp_adjusted_probability="0.73" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="2.67" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1149.2920">
103
- </peptide>
104
- </protein>
105
- </protein_group>
106
- <protein_group group_number="5" probability="1.00">
107
- <protein protein_name="MSORF2042" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="37.4" unique_stripped_peptides="SEESSGGTLASDAQLAALR+GVVSSIVNFGAFVDLGGVDGLVHVSELSWK+AWLEQTQSEVR+HDVDPNEVVSVGDEVEALVLTK+QANEDYTEEFDPSK+VEEGIEGLVHISELSER+YFNDGDIVEGTIVK+VDRDEVLLDIGYK+FAAAEAEAANAPVSNGSSR+THAIGQIVPGK+AWGTIEELK" group_sibling_id="a" total_number_peptides="20" pct_spectrum_ids="1.78">
108
- <annotation protein_description="E: 0.0 mtuberculosis_H37Rv|15608768| rpsA [Mycobacterium tuberculosis H37Rv]|"/>
109
- <peptide peptide_sequence="HDVDPNEVVSVGDEVEALVLTK" 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="9.65" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2364.5920">
110
- </peptide>
111
- <peptide peptide_sequence="HDVDPNEVVSVGDEVEALVLTK" 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="9.65" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2364.5920">
112
- </peptide>
113
- <peptide peptide_sequence="YFNDGDIVEGTIVK" 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="9.65" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1569.6920">
114
- </peptide>
115
- <peptide peptide_sequence="THAIGQIVPGK" charge="2" 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="9.65" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1120.2920">
116
- </peptide>
117
- <peptide peptide_sequence="VEEGIEGLVHISELSER" 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="9.65" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1896.0920">
118
- </peptide>
119
- <peptide peptide_sequence="AWLEQTQSEVR" 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="9.65" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1346.4919">
120
- </peptide>
121
- <peptide peptide_sequence="FAAAEAEAANAPVSNGSSR" 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="9.65" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1819.8920">
122
- </peptide>
123
- <peptide peptide_sequence="QANEDYTEEFDPSK" 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="9.65" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1672.6920">
124
- </peptide>
125
- <peptide peptide_sequence="SEESSGGTLASDAQLAALR" 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="9.65" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1862.9919">
126
- </peptide>
127
- <peptide peptide_sequence="THAIGQIVPGK" charge="1" initial_probability="0.72" nsp_adjusted_probability="0.89" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="9.92" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1120.2920">
128
- </peptide>
129
- <peptide peptide_sequence="AWGTIEELK" charge="1" initial_probability="0.48" nsp_adjusted_probability="0.74" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.16" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1046.1920">
130
- </peptide>
131
- <peptide peptide_sequence="VDRDEVLLDIGYK" charge="2" initial_probability="0.30" nsp_adjusted_probability="0.30" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="10.35" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1534.6920">
132
- </peptide>
133
- <peptide peptide_sequence="GVVSSIVNFGAFVDLGGVDGLVHVSELSWK" 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="10.47" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="3088.4919">
134
- </peptide>
135
- </protein>
136
- </protein_group>
137
- <protein_group group_number="6" probability="1.00">
138
- <protein protein_name="MSORF4304" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="27.0" unique_stripped_peptides="NVAAGANPIALGSGISKAADAVSEALLASATPVDDKK+EAVEDAVAAAK+LAGGVAVIK+AFLDDLAIVTGGQVVNPDVGLLLR+AIAQVATVSSR+TNDVAGDGTTTATVLAQALVR+SFGGPQVTNDGVTIAR+EIDLEDPYENLGAQLVK" group_sibling_id="a" total_number_peptides="13" pct_spectrum_ids="1.21">
139
- <annotation protein_description="E: 0.0 mtuberculosis_H37Rv|15610553| groEL1 [Mycobacterium tuberculosis H37Rv]|"/>
140
- <peptide peptide_sequence="AIAQVATVSSR" 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="5.48" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1102.2920">
141
- </peptide>
142
- <peptide peptide_sequence="SFGGPQVTNDGVTIAR" 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="5.48" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1618.7920">
143
- </peptide>
144
- <peptide peptide_sequence="AFLDDLAIVTGGQVVNPDVGLLLR" 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="5.49" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2495.8921">
145
- </peptide>
146
- <peptide peptide_sequence="EIDLEDPYENLGAQLVK" charge="2" initial_probability="0.98" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.50" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1946.0920">
147
- </peptide>
148
- <peptide peptide_sequence="EAVEDAVAAAK" charge="2" initial_probability="0.92" nsp_adjusted_probability="0.97" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.55" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1073.1920">
149
- </peptide>
150
- <peptide peptide_sequence="TNDVAGDGTTTATVLAQALVR" charge="2" initial_probability="0.87" nsp_adjusted_probability="0.95" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.61" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2074.2920">
151
- </peptide>
152
- <peptide peptide_sequence="EAVEDAVAAAK" charge="1" initial_probability="0.59" nsp_adjusted_probability="0.81" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.89" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1073.1920">
153
- </peptide>
154
- <peptide peptide_sequence="LAGGVAVIK" charge="1" initial_probability="0.58" nsp_adjusted_probability="0.80" weight="0.50" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="6.33" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="826.9920">
155
- <peptide_parent_protein protein_name="MSORF3389"/>
156
- </peptide>
157
- <peptide peptide_sequence="NVAAGANPIALGSGISKAADAVSEALLASATPVDDKK" charge="3" initial_probability="0.05" nsp_adjusted_probability="0.05" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.47" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="3493.8921">
158
- </peptide>
159
- </protein>
160
- </protein_group>
161
- <protein_group group_number="7" probability="1.00">
162
- <protein protein_name="MSORF4271" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="20.4" unique_stripped_peptides="VYAGPDHPHAAQQPIPFEIK+LASAAATLLR" group_sibling_id="a" total_number_peptides="3" pct_spectrum_ids="0.30">
163
- <annotation protein_description="E: 2e-70 mleprae|15827097| 50S ribosomal protein L13 [Mycobacterium leprae]|"/>
164
- <peptide peptide_sequence="VYAGPDHPHAAQQPIPFEIK" 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="1.94" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2215.4919">
165
- </peptide>
166
- <peptide peptide_sequence="LASAAATLLR" 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="1.97" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="986.1920">
167
- </peptide>
168
- <peptide peptide_sequence="VYAGPDHPHAAQQPIPFEIK" charge="2" initial_probability="0.97" nsp_adjusted_probability="0.99" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.97" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2215.4919">
169
- </peptide>
170
- </protein>
171
- </protein_group>
172
- <protein_group group_number="8" probability="1.00">
173
- <protein protein_name="MSORF5691" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="25.1" unique_stripped_peptides="LQPSDLAALGVTNQR+PGWVEHNPVEIWER+LVDDNGGVYFVPAFSGLFAPYWR+TDSIAAALDR+WDPQWTEEQR+SSSAVQSALNAAK+NTYGTGNFLLLNTGTTPVR+IQWILENVPGVR+HQLEHEQILPR" group_sibling_id="a" total_number_peptides="29" pct_spectrum_ids="2.45">
174
- <annotation protein_description="E: 0.0 scoelicolor_A3_2-chr|21219046| glycerol kinase 2 (ATP:glycerol 3-phosphotransferase) (EC 2.7.1.30) [Streptomyces coelicolor A3(2)]|"/>
175
- <peptide peptide_sequence="HQLEHEQILPR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="8.15" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1399.5920">
176
- <peptide_parent_protein protein_name="MSORF6372"/>
177
- </peptide>
178
- <peptide peptide_sequence="NTYGTGNFLLLNTGTTPVR" 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="8.08" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2039.2920">
179
- </peptide>
180
- <peptide peptide_sequence="LVDDNGGVYFVPAFSGLFAPYWR" 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="8.08" n_sibling_peptides_bin="6" n_instances="8" is_contributing_evidence="Y" calc_neutral_pep_mass="2590.8921">
181
- </peptide>
182
- <peptide peptide_sequence="HQLEHEQILPR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="8.15" n_sibling_peptides_bin="6" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1399.5920">
183
- <peptide_parent_protein protein_name="MSORF6372"/>
184
- </peptide>
185
- <peptide peptide_sequence="LQPSDLAALGVTNQR" 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="8.08" n_sibling_peptides_bin="6" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1582.7920">
186
- </peptide>
187
- <peptide peptide_sequence="TDSIAAALDR" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="8.16" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1032.0920">
188
- <peptide_parent_protein protein_name="MSORF6372"/>
189
- </peptide>
190
- <peptide peptide_sequence="SSSAVQSALNAAK" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="8.09" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1233.3920">
191
- </peptide>
192
- <peptide peptide_sequence="SSSAVQSALNAAK" charge="1" initial_probability="0.92" nsp_adjusted_probability="0.97" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="8.15" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1233.3920">
193
- </peptide>
194
- <peptide peptide_sequence="WDPQWTEEQR" charge="2" initial_probability="0.89" nsp_adjusted_probability="0.96" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="8.18" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1374.3920">
195
- </peptide>
196
- <peptide peptide_sequence="IQWILENVPGVR" charge="1" initial_probability="0.39" nsp_adjusted_probability="0.39" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="8.68" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1423.6920">
197
- </peptide>
198
- <peptide peptide_sequence="PGWVEHNPVEIWER" charge="3" initial_probability="0.14" nsp_adjusted_probability="0.14" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="1" n_sibling_peptides="8.94" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1747.8920">
199
- </peptide>
200
- </protein>
201
- </protein_group>
202
- <protein_group group_number="9" probability="1.00">
203
- <protein protein_name="MSORF4649" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="32.8" unique_stripped_peptides="NDEYDNEVYR+IHVEALGGTLTK" group_sibling_id="a" total_number_peptides="7" pct_spectrum_ids="0.68">
204
- <annotation protein_description="E: 1e-30 mtuberculosis_H37Rv|15610384| sahH [Mycobacterium tuberculosis H37Rv]|"/>
205
- <peptide peptide_sequence="IHVEALGGTLTK" charge="1" 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="1.96" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1238.4919">
206
- </peptide>
207
- <peptide peptide_sequence="IHVEALGGTLTK" charge="2" initial_probability="0.98" nsp_adjusted_probability="0.99" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.98" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1238.4919">
208
- </peptide>
209
- <peptide peptide_sequence="NDEYDNEVYR" charge="2" initial_probability="0.98" nsp_adjusted_probability="0.99" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.98" n_sibling_peptides_bin="4" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1316.2920">
210
- </peptide>
211
- </protein>
212
- </protein_group>
213
- <protein_group group_number="10" probability="1.00">
214
- <protein protein_name="MSORF6114" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="20.4" unique_stripped_peptides="IKPAYFTDDEYYEK+TVGLSPEAQQDLVQK" group_sibling_id="a" total_number_peptides="5" pct_spectrum_ids="0.49">
215
- <annotation protein_description="E: 7e-60 mleprae|15826914| conserved hypothetical protein [Mycobacterium leprae]|"/>
216
- <peptide peptide_sequence="IKPAYFTDDEYYEK" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.84" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1781.8920">
217
- </peptide>
218
- <peptide peptide_sequence="TVGLSPEAQQDLVQK" 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="1.84" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1612.7920">
219
- </peptide>
220
- <peptide peptide_sequence="IKPAYFTDDEYYEK" charge="3" initial_probability="0.85" nsp_adjusted_probability="0.94" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.98" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1781.8920">
221
- </peptide>
222
- </protein>
223
- </protein_group>
224
- <protein_group group_number="11" probability="1.00">
225
- <protein protein_name="MSORF5438" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="57.7" unique_stripped_peptides="HTIFGEVVDEESQK+DYSTENASGGTSGPFYDGAVFHR+VVDAIASTPTDR+TVNNFVGLAQGTK+FEDEFHPELQFDK+IALFGNHAPK+SDRPTEPVVIESITIA" group_sibling_id="a" total_number_peptides="12" pct_spectrum_ids="0.97">
226
- <annotation protein_description="E: 2e-78 mtuberculosis_H37Rv|15607151| ppiA [Mycobacterium tuberculosis H37Rv]|"/>
227
- <peptide peptide_sequence="DYSTENASGGTSGPFYDGAVFHR" 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="5.56" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2435.4919">
228
- </peptide>
229
- <peptide peptide_sequence="VVDAIASTPTDR" 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="5.57" n_sibling_peptides_bin="6" n_instances="3" is_contributing_evidence="Y" calc_neutral_pep_mass="1244.3920">
230
- </peptide>
231
- <peptide peptide_sequence="HTIFGEVVDEESQK" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.57" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1617.6920">
232
- </peptide>
233
- <peptide peptide_sequence="TVNNFVGLAQGTK" 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="5.59" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1348.4919">
234
- </peptide>
235
- <peptide peptide_sequence="SDRPTEPVVIESITIA" charge="2" initial_probability="0.95" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.62" n_sibling_peptides_bin="6" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1726.9919">
236
- </peptide>
237
- <peptide peptide_sequence="IALFGNHAPK" charge="2" initial_probability="0.90" nsp_adjusted_probability="0.96" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="5.66" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1067.2920">
238
- </peptide>
239
- <peptide peptide_sequence="HTIFGEVVDEESQK" charge="3" initial_probability="0.53" nsp_adjusted_probability="0.77" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.03" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1617.6920">
240
- </peptide>
241
- <peptide peptide_sequence="FEDEFHPELQFDK" charge="2" initial_probability="0.23" nsp_adjusted_probability="0.23" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="6.33" n_sibling_peptides_bin="6" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1680.7920">
242
- </peptide>
243
- </protein>
244
- </protein_group>
245
- <protein_group group_number="12" probability="1.00">
246
- <protein protein_name="MSORF2285" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="14.6" unique_stripped_peptides="FLLDQPTTSAGR+HPDSDIFLDDVTVSR" group_sibling_id="a" total_number_peptides="8" pct_spectrum_ids="0.68">
247
- <annotation protein_description="E: 5e-68 mtuberculosis_H37Rv|15608964| hypothetical protein Rv1827 [Mycobacterium tuberculosis H37Rv]|"/>
248
- <peptide peptide_sequence="HPDSDIFLDDVTVSR" 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="1.94" n_sibling_peptides_bin="4" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1715.7920">
249
- </peptide>
250
- <peptide peptide_sequence="FLLDQPTTSAGR" 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="1.95" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1305.4919">
251
- </peptide>
252
- <peptide peptide_sequence="HPDSDIFLDDVTVSR" charge="3" initial_probability="0.95" nsp_adjusted_probability="0.98" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="1.98" n_sibling_peptides_bin="4" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1715.7920">
253
- </peptide>
254
- </protein>
255
- </protein_group>
256
- <protein_group group_number="13" probability="1.00">
257
- <protein protein_name="MSORF7435" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="7.6" unique_stripped_peptides="LNFSHGDYSDHEAAYK+IIQAVEDNSVVVPPLTHVPR" group_sibling_id="a" total_number_peptides="3" pct_spectrum_ids="0.28">
258
- <annotation protein_description="E: 0.0 mtuberculosis_H37Rv|15608755| pykA [Mycobacterium tuberculosis H37Rv]|"/>
259
- <peptide peptide_sequence="IIQAVEDNSVVVPPLTHVPR" 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="0.99" n_sibling_peptides_bin="3" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2183.4919">
260
- </peptide>
261
- <peptide peptide_sequence="LNFSHGDYSDHEAAYK" 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="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1853.8920">
262
- </peptide>
263
- </protein>
264
- </protein_group>
265
- <protein_group group_number="14" probability="1.00">
266
- <protein protein_name="MSORF3389" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="42.0" unique_stripped_peptides="SALQNAASIAALFLTTEAVVADKPEK+WGAPTITNDGVSIAK+GYISGYFVTDAER+QEAVLEDPYILLVSSK+VSNLPAGHGLNAATGEYEDLLAAGVADPVK+LAGGVAVIK+DLLPLLEK+AEIENSDSDYDR+QIALNGGLEPGVVAEK+GLNSLADAVK+KTDDVAGDGTTTATVLAQALVR+EIELEDPYEK+TDDVAGDGTTTATVLAQALVR+VTETLLK+VALSAPLK+NVAAGANPLGLK+DETTIVEGAGDAEAIQGR+AGAATEVELK" group_sibling_id="a" total_number_peptides="50" pct_spectrum_ids="4.47">
267
- <annotation protein_description="E: 0.0 mleprae|15827082| 60 kDa chaperonin 2 [Mycobacterium leprae]|"/>
268
- <peptide peptide_sequence="EIELEDPYEK" charge="1" 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="18.63" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1264.3920">
269
- </peptide>
270
- <peptide peptide_sequence="VSNLPAGHGLNAATGEYEDLLAAGVADPVK" 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="18.63" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2950.2920">
271
- </peptide>
272
- <peptide peptide_sequence="QEAVLEDPYILLVSSK" 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="18.63" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1804.0920">
273
- </peptide>
274
- <peptide peptide_sequence="TDDVAGDGTTTATVLAQALVR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" peptide_group_designator="c" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.63" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="2075.2920">
275
- </peptide>
276
- <peptide peptide_sequence="KTDDVAGDGTTTATVLAQALVR" 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="18.63" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2203.3921">
277
- </peptide>
278
- <peptide peptide_sequence="GYISGYFVTDAER" 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="18.63" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1477.5920">
279
- </peptide>
280
- <peptide peptide_sequence="QIALNGGLEPGVVAEK" 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="18.63" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1594.7920">
281
- </peptide>
282
- <peptide peptide_sequence="DETTIVEGAGDAEAIQGR" 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="18.63" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="1831.8920">
283
- </peptide>
284
- <peptide peptide_sequence="WGAPTITNDGVSIAK" 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="18.63" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1529.6920">
285
- </peptide>
286
- <peptide peptide_sequence="AEIENSDSDYDR" charge="2" initial_probability="0.99" nsp_adjusted_probability="1.00" peptide_group_designator="f" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.63" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1413.3920">
287
- </peptide>
288
- <peptide peptide_sequence="VSNLPAGHGLNAATGEYEDLLAAGVADPVK" charge="3" initial_probability="0.99" nsp_adjusted_probability="1.00" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.64" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2950.2920">
289
- </peptide>
290
- <peptide peptide_sequence="AGAATEVELK" charge="2" initial_probability="0.98" nsp_adjusted_probability="0.99" peptide_group_designator="e" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.64" n_sibling_peptides_bin="7" n_instances="7" is_contributing_evidence="Y" calc_neutral_pep_mass="988.0920">
291
- </peptide>
292
- <peptide peptide_sequence="EIELEDPYEK" charge="2" initial_probability="0.94" nsp_adjusted_probability="0.98" peptide_group_designator="b" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.69" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1264.3920">
293
- </peptide>
294
- <peptide peptide_sequence="VALSAPLK" charge="1" initial_probability="0.93" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.70" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="797.9920">
295
- </peptide>
296
- <peptide peptide_sequence="TDDVAGDGTTTATVLAQALVR" charge="3" initial_probability="0.87" nsp_adjusted_probability="0.95" peptide_group_designator="c" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.75" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2075.2920">
297
- </peptide>
298
- <peptide peptide_sequence="SALQNAASIAALFLTTEAVVADKPEK" charge="3" initial_probability="0.86" nsp_adjusted_probability="0.95" peptide_group_designator="d" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.76" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2658.9919">
299
- </peptide>
300
- <peptide peptide_sequence="DLLPLLEK" charge="1" initial_probability="0.76" nsp_adjusted_probability="0.91" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.86" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="940.1920">
301
- </peptide>
302
- <peptide peptide_sequence="SALQNAASIAALFLTTEAVVADKPEK" charge="2" initial_probability="0.74" nsp_adjusted_probability="0.90" peptide_group_designator="d" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.88" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2658.9919">
303
- </peptide>
304
- <peptide peptide_sequence="NVAAGANPLGLK" charge="2" initial_probability="0.64" nsp_adjusted_probability="0.84" peptide_group_designator="g" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="18.99" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1124.2920">
305
- </peptide>
306
- <peptide peptide_sequence="LAGGVAVIK" charge="1" initial_probability="0.58" nsp_adjusted_probability="0.80" weight="0.50" is_nondegenerate_evidence="N" n_tryptic_termini="2" n_sibling_peptides="19.19" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="826.9920">
307
- <peptide_parent_protein protein_name="MSORF4304"/>
308
- </peptide>
309
- <peptide peptide_sequence="GLNSLADAVK" charge="1" initial_probability="0.56" nsp_adjusted_probability="0.79" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.07" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="987.0920">
310
- </peptide>
311
- <peptide peptide_sequence="AGAATEVELK" charge="1" initial_probability="0.50" nsp_adjusted_probability="0.75" peptide_group_designator="e" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.12" n_sibling_peptides_bin="7" n_instances="4" is_contributing_evidence="Y" calc_neutral_pep_mass="988.0920">
312
- </peptide>
313
- <peptide peptide_sequence="AEIENSDSDYDR" charge="1" initial_probability="0.33" nsp_adjusted_probability="0.33" peptide_group_designator="f" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.29" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1413.3920">
314
- </peptide>
315
- <peptide peptide_sequence="NVAAGANPLGLK" charge="1" initial_probability="0.11" nsp_adjusted_probability="0.11" peptide_group_designator="g" weight="1.00" is_nondegenerate_evidence="Y" n_tryptic_termini="2" n_sibling_peptides="19.52" n_sibling_peptides_bin="7" n_instances="2" is_contributing_evidence="N" calc_neutral_pep_mass="1124.2920">
316
- </peptide>
317
- <peptide peptide_sequence="VTETLLK" 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="19.63" n_sibling_peptides_bin="7" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="802.9920">
318
- </peptide>
319
- </protein>
320
- </protein_group>
321
- </protein_summary>