mspire 0.2.4 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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>