mspire 0.2.4 → 0.3.0

Sign up to get free protection for your applications and to get access to all the features.
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/corrupted_900.srf ADDED
Binary file
data/test_files/head_of_7MIX.srf ADDED
Binary file
data/test_files/interact-opd1_mods_small-prot.xml ADDED
@@ -0,0 +1,304 @@
1
+ <?xml version="1.0" encoding="UTF-8"?>
2
+ <?xml-stylesheet type="text/xsl" href="/work/tpp-data/interact-opd1_mods-prot.xsl"?>
3
+ <protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/protXML /tools/bin/TPP/tpp/bin/../schema/protXML_v4.xsd" summary_xml="/work/tpp-data/interact-opd1_mods-prot.xml">
4
+ <protein_summary_header reference_database="/project/marcotte/marcotte/ms/database/ecoli_K12_ncbi_20060321.fasta" residue_substitution_list="I -> L" source_files="/work/tpp-data/interact-opd1_mods.xml" source_files_alt="/work/tpp-data/interact-opd1_mods.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="439.0" num_input_1_spectra="19" num_input_2_spectra="585" num_input_3_spectra="1039" initial_min_peptide_prob="0.05" total_no_spectrum_ids="557.5" sample_enzyme="trypsin">
5
+ <program_details analysis="proteinprophet" time="2007-04-24T13:37:22" version="4.0(TPP v2.9 GALE rev.2, Build 200703091101)">
6
+ <proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" initial_peptide_wt_iters="2" nsp_distribution_iters="1" final_peptide_wt_iters="1" run_options="XML_INPUT">
7
+ <nsp_information neighboring_bin_smoothing="Y">
8
+ <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_excl="0.10" pos_freq="0.529" neg_freq="0.542" pos_to_neg_ratio="0.98"/>
9
+ <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.191" neg_freq="0.181" pos_to_neg_ratio="1.06"/>
10
+ <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.100" neg_freq="0.096" pos_to_neg_ratio="1.04" alt_pos_to_neg_ratio="1.06"/>
11
+ <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.110" neg_freq="0.109" pos_to_neg_ratio="1.01" alt_pos_to_neg_ratio="1.06"/>
12
+ <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.052" neg_freq="0.053" pos_to_neg_ratio="0.98" alt_pos_to_neg_ratio="1.06"/>
13
+ <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.011" neg_freq="0.012" pos_to_neg_ratio="0.93" alt_pos_to_neg_ratio="1.06"/>
14
+ <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.004" neg_freq="0.004" pos_to_neg_ratio="0.97" alt_pos_to_neg_ratio="1.06"/>
15
+ <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.004" neg_freq="0.004" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.06"/>
16
+ </nsp_information> <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.652" predicted_num_correct="439" predicted_num_incorrect="822" />
17
+ <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.443" predicted_num_correct="439" predicted_num_incorrect="349" />
18
+ <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.443" predicted_num_correct="439" predicted_num_incorrect="349" />
19
+ <protein_summary_data_filter min_probability="0.30" sensitivity="0.910" false_positive_error_rate="0.363" predicted_num_correct="400" predicted_num_incorrect="228" />
20
+ <protein_summary_data_filter min_probability="0.40" sensitivity="0.815" false_positive_error_rate="0.294" predicted_num_correct="358" predicted_num_incorrect="149" />
21
+ <protein_summary_data_filter min_probability="0.50" sensitivity="0.724" false_positive_error_rate="0.236" predicted_num_correct="318" predicted_num_incorrect="98" />
22
+ <protein_summary_data_filter min_probability="0.60" sensitivity="0.626" false_positive_error_rate="0.182" predicted_num_correct="275" predicted_num_incorrect="61" />
23
+ <protein_summary_data_filter min_probability="0.70" sensitivity="0.491" false_positive_error_rate="0.117" predicted_num_correct="216" predicted_num_incorrect="28" />
24
+ <protein_summary_data_filter min_probability="0.80" sensitivity="0.394" false_positive_error_rate="0.074" predicted_num_correct="173" predicted_num_incorrect="14" />
25
+ <protein_summary_data_filter min_probability="0.90" sensitivity="0.263" false_positive_error_rate="0.030" predicted_num_correct="115" predicted_num_incorrect="4" />
26
+ <protein_summary_data_filter min_probability="0.95" sensitivity="0.185" false_positive_error_rate="0.009" predicted_num_correct="81" predicted_num_incorrect="1" />
27
+ <protein_summary_data_filter min_probability="0.96" sensitivity="0.172" false_positive_error_rate="0.005" predicted_num_correct="76" predicted_num_incorrect="0" />
28
+ <protein_summary_data_filter min_probability="0.97" sensitivity="0.168" false_positive_error_rate="0.004" predicted_num_correct="74" predicted_num_incorrect="0" />
29
+ <protein_summary_data_filter min_probability="0.98" sensitivity="0.166" false_positive_error_rate="0.004" predicted_num_correct="73" predicted_num_incorrect="0" />
30
+ <protein_summary_data_filter min_probability="0.99" sensitivity="0.150" false_positive_error_rate="0.002" predicted_num_correct="66" predicted_num_incorrect="0" />
31
+ <protein_summary_data_filter min_probability="1.00" sensitivity="0.116" false_positive_error_rate="0.000" predicted_num_correct="51" predicted_num_incorrect="0" />
32
+ </proteinprophet_details>
33
+ </program_details>
34
+ </protein_summary_header>
35
+ <dataset_derivation generation_no="0">
36
+ </dataset_derivation>
37
+ <protein_group group_number="1" probability="1.00">
38
+ <protein protein_name="gi|16130155|ref|NP_416722.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="4.8" unique_stripped_peptides="IISDILDFSKIESEQLK+VLERIRMLILNAILLNVLAGAALFTLAR+MLILNAILLNVLAGAALFTLAR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.23">
39
+ <annotation protein_description="hybrid sensory histidine kinase in two-component regulatory system with RcsB, regulates capsule biosynthesis, cell division genes, OsmC expression [Escherichia coli K12]"/>
40
+ <peptide peptide_sequence="MLILNAILLNVLAGAALFTLAR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.28" n_sibling_peptides_bin="2" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2311.88233542">
41
+ </peptide>
42
+ <peptide peptide_sequence="VLERIRMLILNAILLNVLAGAALFTLAR" charge="3" initial_probability="0.14" nsp_adjusted_probability="0.14" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.14" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="3078.81764942">
43
+ </peptide>
44
+ <peptide peptide_sequence="IISDILDFSKIESEQLK" charge="3" initial_probability="0.14" nsp_adjusted_probability="0.14" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.14" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2138.21256242">
45
+ <modification_info modified_peptide="IISDILDFS[167]KIESE[167]QLK">
46
+ <mod_aminoacid_mass position="9" mass="167.058100"/>
47
+ <mod_aminoacid_mass position="14" mass="167.058100"/>
48
+ </modification_info>
49
+ </peptide>
50
+ </protein>
51
+ </protein_group>
52
+ <protein_group group_number="2" probability="1.00">
53
+ <protein protein_name="gi|16130444|ref|NP_417014.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="4.9" unique_stripped_peptides="TGTSYGYR+REILTLYLNR+GRLPPRSSLAMIVVDHTDMR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.23">
54
+ <annotation protein_description="penicillin binding protein 1C (PBP 1C) [Escherichia coli K12]"/>
55
+ <peptide peptide_sequence="TGTSYGYR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.30" n_sibling_peptides_bin="2" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1143.87892542">
56
+ <modification_info modified_peptide="TGTS[167]YG[243]YR">
57
+ <mod_aminoacid_mass position="4" mass="167.058100"/>
58
+ <mod_aminoacid_mass position="6" mass="243.155900"/>
59
+ </modification_info>
60
+ </peptide>
61
+ <peptide peptide_sequence="REILTLYLNR" charge="3" initial_probability="0.17" nsp_adjusted_probability="0.17" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.13" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1290.51699942">
62
+ </peptide>
63
+ <peptide peptide_sequence="GRLPPRSSLAMIVVDHTDMR" charge="3" initial_probability="0.13" nsp_adjusted_probability="0.13" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.17" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2427.60190742">
64
+ <modification_info modified_peptide="GRLPPRS[167]SLAMI[147]VVDHTDM[181]R">
65
+ <mod_aminoacid_mass position="7" mass="167.058100"/>
66
+ <mod_aminoacid_mass position="12" mass="147.192000"/>
67
+ <mod_aminoacid_mass position="19" mass="181.085000"/>
68
+ </modification_info>
69
+ </peptide>
70
+ </protein>
71
+ </protein_group>
72
+ <protein_group group_number="3" probability="1.00">
73
+ <protein protein_name="gi|16128036|ref|NP_414584.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="3.8" unique_stripped_peptides="LVVSVGRGIGSK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
74
+ <annotation protein_description="putative electron transfer flavoprotein subunit alpha [Escherichia coli K12]"/>
75
+ <peptide peptide_sequence="LVVSVGRGIGSK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1331.35545442">
76
+ <modification_info modified_peptide="LVVS[167]VGRGIGSK[167]">
77
+ <mod_aminoacid_mass position="4" mass="167.058100"/>
78
+ <mod_aminoacid_mass position="12" mass="167.058100"/>
79
+ </modification_info>
80
+ </peptide>
81
+ </protein>
82
+ </protein_group>
83
+ <protein_group group_number="4" probability="1.00">
84
+ <protein protein_name="gi|16129057|ref|NP_415612.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="20.5" unique_stripped_peptides="ITTVQAAIDYINGHQA" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
85
+ <annotation protein_description="acyl carrier protein [Escherichia coli K12]"/>
86
+ <peptide peptide_sequence="ITTVQAAIDYINGHQA" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1714.88094942">
87
+ </peptide>
88
+ </protein>
89
+ </protein_group>
90
+ <protein_group group_number="5" probability="1.00">
91
+ <protein protein_name="gi|16129208|ref|NP_415763.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="2.7" unique_stripped_peptides="ERVKAMMLK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
92
+ <annotation protein_description="homolog of Salmonella ATP-binding protein of oligopeptide ABC transport system [Escherichia coli K12]"/>
93
+ <peptide peptide_sequence="ERVKAMMLK" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1105.42412242">
94
+ </peptide>
95
+ </protein>
96
+ </protein_group>
97
+ <protein_group group_number="6" probability="1.00">
98
+ <protein protein_name="gi|16131948|ref|NP_418546.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="2.4" unique_stripped_peptides="VWTGGGDEETLSK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
99
+ <annotation protein_description="fumarase B (fumarate hydratase class I), anaerobic isozyme [Escherichia coli K12]"/>
100
+ <peptide peptide_sequence="VWTGGGDEETLSK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1458.42667342">
101
+ <modification_info modified_peptide="VWT[181]GGGDEETLSK">
102
+ <mod_aminoacid_mass position="3" mass="181.085000"/>
103
+ </modification_info>
104
+ </peptide>
105
+ </protein>
106
+ </protein_group>
107
+ <protein_group group_number="7" probability="1.00">
108
+ <protein protein_name="gi|16132083|ref|NP_418682.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="6.8" unique_stripped_peptides="YLVRETLKSQLAILFILLLIFFCQK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
109
+ <annotation protein_description="putative transmembrane protein, transport [Escherichia coli K12]"/>
110
+ <peptide peptide_sequence="YLVRETLKSQLAILFILLLIFFCQK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="3013.73766242">
111
+ </peptide>
112
+ </protein>
113
+ </protein_group>
114
+ <protein_group group_number="8" probability="1.00">
115
+ <protein protein_name="gi|16128931|ref|NP_415484.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="5.0" unique_stripped_peptides="YWFKLADPQTR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
116
+ <annotation protein_description="hypothetical protein b0964 [Escherichia coli K12]"/>
117
+ <peptide peptide_sequence="YWFKLADPQTR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1584.56813542">
118
+ <modification_info modified_peptide="Y[243]WFKLADPQTR[181]">
119
+ <mod_aminoacid_mass position="1" mass="243.155900"/>
120
+ <mod_aminoacid_mass position="11" mass="181.085000"/>
121
+ </modification_info>
122
+ </peptide>
123
+ </protein>
124
+ </protein_group>
125
+ <protein_group group_number="9" probability="1.00">
126
+ <protein protein_name="gi|16130395|ref|NP_416965.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="2.8" unique_stripped_peptides="KVYVQAAAPYR+DWSERDSKTGTSFAIIER" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.24">
127
+ <annotation protein_description="aminoglycoside efflux pump [Escherichia coli K12]"/>
128
+ <peptide peptide_sequence="DWSERDSKTGTSFAIIER" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.37" n_sibling_peptides_bin="2" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2338.17884642">
129
+ <modification_info modified_peptide="DWS[167]ERDSK[167]TGT[181]SFAIIER">
130
+ <mod_aminoacid_mass position="3" mass="167.058100"/>
131
+ <mod_aminoacid_mass position="8" mass="167.058100"/>
132
+ <mod_aminoacid_mass position="11" mass="181.085000"/>
133
+ </modification_info>
134
+ </peptide>
135
+ <peptide peptide_sequence="KVYVQAAAPYR" charge="2" initial_probability="0.37" nsp_adjusted_probability="0.37" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1265.46600042">
136
+ </peptide>
137
+ </protein>
138
+ </protein_group>
139
+ <protein_group group_number="10" probability="1.00">
140
+ <protein protein_name="gi|16128164|ref|NP_414713.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="7.5" unique_stripped_peptides="VFNMNKPGALRRVVMGEK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
141
+ <annotation protein_description="uridylate kinase [Escherichia coli K12]"/>
142
+ <peptide peptide_sequence="VFNMNKPGALRRVVMGEK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2062.47270042">
143
+ <modification_info modified_peptide="VFNMNKPGALRRVVM[147]GEK">
144
+ <mod_aminoacid_mass position="15" mass="147.192000"/>
145
+ </modification_info>
146
+ </peptide>
147
+ </protein>
148
+ </protein_group>
149
+ <protein_group group_number="11" probability="1.00">
150
+ <protein protein_name="gi|16130313|ref|NP_416882.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="9.4" unique_stripped_peptides="ESYVMPMNITEFCSK+MTFVYTRR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.19">
151
+ <annotation protein_description="putative 2-component transcriptional regulator [Escherichia coli K12]"/>
152
+ <peptide peptide_sequence="MTFVYTRR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1313.21373842">
153
+ <modification_info modified_peptide="MT[181]FVYT[243]RR[181]">
154
+ <mod_aminoacid_mass position="2" mass="181.085000"/>
155
+ <mod_aminoacid_mass position="6" mass="243.155900"/>
156
+ <mod_aminoacid_mass position="8" mass="181.085000"/>
157
+ </modification_info>
158
+ </peptide>
159
+ <peptide peptide_sequence="ESYVMPMNITEFCSK" charge="3" initial_probability="0.07" nsp_adjusted_probability="0.07" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1955.03132942">
160
+ <modification_info modified_peptide="ESYVMPM[147]NITE[181]FCSK">
161
+ <mod_aminoacid_mass position="7" mass="147.192000"/>
162
+ <mod_aminoacid_mass position="11" mass="181.085000"/>
163
+ </modification_info>
164
+ </peptide>
165
+ </protein>
166
+ </protein_group>
167
+ <protein_group group_number="12" probability="1.00">
168
+ <protein protein_name="gi|16130348|ref|NP_416917.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="5.8" unique_stripped_peptides="LYNGDERIETRDEELALAQSA" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
169
+ <annotation protein_description="ATP-binding component of sulfate permease A protein; chromate resistance [Escherichia coli K12]"/>
170
+ <peptide peptide_sequence="LYNGDERIETRDEELALAQSA" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2633.46970342">
171
+ <modification_info modified_peptide="LY[243]NGDERIETR[181]DEELALAQSA">
172
+ <mod_aminoacid_mass position="2" mass="243.155900"/>
173
+ <mod_aminoacid_mass position="11" mass="181.085000"/>
174
+ </modification_info>
175
+ </peptide>
176
+ </protein>
177
+ </protein_group>
178
+ <protein_group group_number="13" probability="1.00">
179
+ <protein protein_name="gi|16129981|ref|NP_416545.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="10.8" unique_stripped_peptides="ALYTVVTEGKAGETYNIGGHNEK+SGAYQSWIEQNYEGRQ" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.23">
180
+ <annotation protein_description="dTDP-glucose 4,6 dehydratase [Escherichia coli K12]"/>
181
+ <peptide peptide_sequence="SGAYQSWIEQNYEGRQ" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.22" n_sibling_peptides_bin="1" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2155.91682242">
182
+ <modification_info modified_peptide="S[167]GAYQ[243]SWI[167]EQNYEGRQ">
183
+ <mod_aminoacid_mass position="1" mass="167.058100"/>
184
+ <mod_aminoacid_mass position="5" mass="243.155900"/>
185
+ <mod_aminoacid_mass position="8" mass="167.058100"/>
186
+ </modification_info>
187
+ </peptide>
188
+ <peptide peptide_sequence="ALYTVVTEGKAGETYNIGGHNEK" charge="3" initial_probability="0.22" nsp_adjusted_probability="0.22" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2691.59398542">
189
+ <modification_info modified_peptide="ALYTVVT[181]EGKAGETY[181]NI[243]GGHNEK">
190
+ <mod_aminoacid_mass position="7" mass="181.085000"/>
191
+ <mod_aminoacid_mass position="15" mass="181.085000"/>
192
+ <mod_aminoacid_mass position="17" mass="243.155900"/>
193
+ </modification_info>
194
+ </peptide>
195
+ <peptide peptide_sequence="SGAYQSWIEQNYEGRQ" charge="3" initial_probability="0.05" nsp_adjusted_probability="0.05" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.22" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2155.91682242">
196
+ <modification_info modified_peptide="SGAY[243]QSW[167]IEQNYEG[243]RQ">
197
+ <mod_aminoacid_mass position="4" mass="243.155900"/>
198
+ <mod_aminoacid_mass position="7" mass="167.058100"/>
199
+ <mod_aminoacid_mass position="14" mass="243.155900"/>
200
+ </modification_info>
201
+ </peptide>
202
+ </protein>
203
+ </protein_group>
204
+ <protein_group group_number="14" probability="1.00">
205
+ <protein protein_name="gi|16129535|ref|NP_416094.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="5.6" unique_stripped_peptides="ISPVIAAIHR+ISPVIAAIHREYKQTWK" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.23">
206
+ <annotation protein_description="Qin prophage [Escherichia coli K12]"/>
207
+ <peptide peptide_sequence="ISPVIAAIHR" charge="1" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.29" n_sibling_peptides_bin="2" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1076.29756142">
208
+ </peptide>
209
+ <peptide peptide_sequence="ISPVIAAIHREYKQTWK" charge="2" initial_probability="0.29" nsp_adjusted_probability="0.29" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2280.31677642">
210
+ <modification_info modified_peptide="IS[167]PVIAAIHREYK[243]QTWK[181]">
211
+ <mod_aminoacid_mass position="2" mass="167.058100"/>
212
+ <mod_aminoacid_mass position="13" mass="243.155900"/>
213
+ <mod_aminoacid_mass position="17" mass="181.085000"/>
214
+ </modification_info>
215
+ </peptide>
216
+ </protein>
217
+ </protein_group>
218
+ <protein_group group_number="15" probability="1.00">
219
+ <protein protein_name="gi|16130915|ref|NP_417491.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="1.1" unique_stripped_peptides="YTESRLSK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
220
+ <annotation protein_description="DNA topoisomerase IV subunit A [Escherichia coli K12]"/>
221
+ <peptide peptide_sequence="YTESRLSK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1223.02072642">
222
+ <modification_info modified_peptide="Y[243]TE[181]SRLSK">
223
+ <mod_aminoacid_mass position="1" mass="243.155900"/>
224
+ <mod_aminoacid_mass position="3" mass="181.085000"/>
225
+ </modification_info>
226
+ </peptide>
227
+ </protein>
228
+ </protein_group>
229
+ <protein_group group_number="16" probability="1.00">
230
+ <protein protein_name="gi|16130312|ref|NP_416881.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="3.2" unique_stripped_peptides="AALMLICLFFLIRIRLFR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
231
+ <annotation protein_description="putative sensor protein [Escherichia coli K12]"/>
232
+ <peptide peptide_sequence="AALMLICLFFLIRIRLFR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2225.86097542">
233
+ <modification_info modified_peptide="AALM[147]LICLFFLIRIRLFR">
234
+ <mod_aminoacid_mass position="4" mass="147.192000"/>
235
+ </modification_info>
236
+ </peptide>
237
+ </protein>
238
+ </protein_group>
239
+ <protein_group group_number="17" probability="1.00">
240
+ <protein protein_name="gi|16130839|ref|NP_417413.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="1.5" unique_stripped_peptides="ARLASQGSGK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
241
+ <annotation protein_description="arginine decarboxylase [Escherichia coli K12]"/>
242
+ <peptide peptide_sequence="ARLASQGSGK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1134.03716342">
243
+ <modification_info modified_peptide="ARLAS[167]QGSG[167]K">
244
+ <mod_aminoacid_mass position="5" mass="167.058100"/>
245
+ <mod_aminoacid_mass position="9" mass="167.058100"/>
246
+ </modification_info>
247
+ </peptide>
248
+ </protein>
249
+ </protein_group>
250
+ <protein_group group_number="18" probability="1.00">
251
+ <protein protein_name="gi|16129084|ref|NP_415639.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="11.1" unique_stripped_peptides="FIILLSLLILLPLTAASKPLIPIMK+FTTR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
252
+ <annotation protein_description="hypothetical protein b1121 [Escherichia coli K12]"/>
253
+ <peptide peptide_sequence="FIILLSLLILLPLTAASKPLIPIMK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2748.55254142">
254
+ <modification_info modified_peptide="FIILLSLLILLPLTAASKPLIPIM[147]K">
255
+ <mod_aminoacid_mass position="24" mass="147.192000"/>
256
+ </modification_info>
257
+ </peptide>
258
+ <peptide peptide_sequence="FTTR" charge="2" initial_probability="0.00" nsp_adjusted_probability="0.00" weight="0.82" is_nondegenerate_evidence="N" n_enzymatic_termini="1" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="683.54471542">
259
+ <modification_info modified_peptide="FT[181]TR[181]">
260
+ <mod_aminoacid_mass position="2" mass="181.085000"/>
261
+ <mod_aminoacid_mass position="4" mass="181.085000"/>
262
+ </modification_info>
263
+ <peptide_parent_protein protein_name="gi|16130538|ref|NP_417109.1|"/>
264
+ <peptide_parent_protein protein_name="gi|16129756|ref|NP_416316.1|"/>
265
+ <peptide_parent_protein protein_name="gi|16130018|ref|NP_416582.1|"/>
266
+ <peptide_parent_protein protein_name="gi|16131037|ref|NP_417614.1|"/>
267
+ <peptide_parent_protein protein_name="gi|16128160|ref|NP_414709.1|"/>
268
+ <peptide_parent_protein protein_name="gi|90111095|ref|NP_414717.2|"/>
269
+ <peptide_parent_protein protein_name="gi|90111095|ref|NP_414717.2|"/>
270
+ <peptide_parent_protein protein_name="gi|16131037|ref|NP_417614.1|"/>
271
+ <peptide_parent_protein protein_name="gi|16131912|ref|NP_418510.1|"/>
272
+ <peptide_parent_protein protein_name="gi|16128353|ref|NP_414902.1|"/>
273
+ <peptide_parent_protein protein_name="gi|16128899|ref|NP_415452.1|"/>
274
+ </peptide>
275
+ </protein>
276
+ </protein_group>
277
+ <protein_group group_number="19" probability="1.00">
278
+ <protein protein_name="gi|16128701|ref|NP_415254.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="1.7" unique_stripped_peptides="QALRGMRRPLVVMSPK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.18">
279
+ <annotation protein_description="2-oxoglutarate decarboxylase, component of the 2-oxoglutarate dehydrogenase complex, thiamin-binding [Escherichia coli K12]"/>
280
+ <peptide peptide_sequence="QALRGMRRPLVVMSPK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1855.28893742">
281
+ <modification_info modified_peptide="QALRGM[147]RRPLVVMSPK">
282
+ <mod_aminoacid_mass position="6" mass="147.192000"/>
283
+ </modification_info>
284
+ </peptide>
285
+ </protein>
286
+ </protein_group>
287
+ <protein_group group_number="20" probability="1.00">
288
+ <protein protein_name="gi|16128265|ref|NP_414814.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="15.1" unique_stripped_peptides="SHHSTAK+MQNATNFLARLMSCK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.20">
289
+ <annotation protein_description="CP4-6 prophage [Escherichia coli K12]"/>
290
+ <peptide peptide_sequence="SHHSTAK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.14" n_sibling_peptides_bin="1" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1006.74548642">
291
+ <modification_info modified_peptide="S[167]HHST[167]AK[181]">
292
+ <mod_aminoacid_mass position="1" mass="167.058100"/>
293
+ <mod_aminoacid_mass position="5" mass="167.058100"/>
294
+ <mod_aminoacid_mass position="7" mass="181.085000"/>
295
+ </modification_info>
296
+ </peptide>
297
+ <peptide peptide_sequence="MQNATNFLARLMSCK" charge="2" initial_probability="0.14" nsp_adjusted_probability="0.14" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1808.05785042">
298
+ <modification_info modified_peptide="MQNATNFLARLMS[167]CK">
299
+ <mod_aminoacid_mass position="13" mass="167.058100"/>
300
+ </modification_info>
301
+ </peptide>
302
+ </protein>
303
+ </protein_group>
304
+ </protein_summary>