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/4-03-03_small-prot.xml ADDED
@@ -0,0 +1,321 @@
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <!DOCTYPE protein_summary SYSTEM "http://localhost/isb-bin/ProteinProphet_v1.9.dtd">
3
+ <?xml-stylesheet type="text/xsl" href="/isb/interact-4-03-03-prot.xsl"?>
4
+ <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>