mspire 0.4.9 → 0.5.0

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Files changed (255) hide show
  1. data/README +27 -17
  2. data/changelog.txt +31 -62
  3. data/lib/ms/calc.rb +32 -0
  4. data/lib/ms/data/interleaved.rb +60 -0
  5. data/lib/ms/data/lazy_io.rb +73 -0
  6. data/lib/ms/data/lazy_string.rb +15 -0
  7. data/lib/ms/data/simple.rb +59 -0
  8. data/lib/ms/data/transposed.rb +41 -0
  9. data/lib/ms/data.rb +57 -0
  10. data/lib/ms/format/format_error.rb +12 -0
  11. data/lib/ms/spectrum.rb +25 -384
  12. data/lib/ms/support/binary_search.rb +126 -0
  13. data/lib/ms.rb +10 -10
  14. metadata +38 -350
  15. data/INSTALL +0 -58
  16. data/README.rdoc +0 -18
  17. data/Rakefile +0 -330
  18. data/bin/aafreqs.rb +0 -23
  19. data/bin/bioworks2excel.rb +0 -14
  20. data/bin/bioworks_to_pepxml.rb +0 -148
  21. data/bin/bioworks_to_pepxml_gui.rb +0 -225
  22. data/bin/fasta_shaker.rb +0 -5
  23. data/bin/filter_and_validate.rb +0 -5
  24. data/bin/gi2annot.rb +0 -14
  25. data/bin/id_class_anal.rb +0 -112
  26. data/bin/id_precision.rb +0 -172
  27. data/bin/ms_to_lmat.rb +0 -67
  28. data/bin/pepproph_filter.rb +0 -16
  29. data/bin/prob_validate.rb +0 -6
  30. data/bin/protein_summary.rb +0 -6
  31. data/bin/protxml2prots_peps.rb +0 -32
  32. data/bin/raw_to_mzXML.rb +0 -55
  33. data/bin/run_percolator.rb +0 -122
  34. data/bin/sqt_group.rb +0 -26
  35. data/bin/srf_group.rb +0 -27
  36. data/bin/srf_to_sqt.rb +0 -40
  37. data/lib/align/chams.rb +0 -78
  38. data/lib/align.rb +0 -154
  39. data/lib/archive/targz.rb +0 -94
  40. data/lib/bsearch.rb +0 -120
  41. data/lib/core_extensions.rb +0 -16
  42. data/lib/fasta.rb +0 -626
  43. data/lib/gi.rb +0 -124
  44. data/lib/group_by.rb +0 -10
  45. data/lib/index_by.rb +0 -11
  46. data/lib/merge_deep.rb +0 -21
  47. data/lib/ms/converter/mzxml.rb +0 -77
  48. data/lib/ms/gradient_program.rb +0 -170
  49. data/lib/ms/msrun.rb +0 -244
  50. data/lib/ms/msrun_index.rb +0 -108
  51. data/lib/ms/parser/mzdata/axml.rb +0 -67
  52. data/lib/ms/parser/mzdata/dom.rb +0 -175
  53. data/lib/ms/parser/mzdata/libxml.rb +0 -7
  54. data/lib/ms/parser/mzdata.rb +0 -31
  55. data/lib/ms/parser/mzxml/axml.rb +0 -70
  56. data/lib/ms/parser/mzxml/dom.rb +0 -182
  57. data/lib/ms/parser/mzxml/hpricot.rb +0 -253
  58. data/lib/ms/parser/mzxml/libxml.rb +0 -19
  59. data/lib/ms/parser/mzxml/regexp.rb +0 -122
  60. data/lib/ms/parser/mzxml/rexml.rb +0 -72
  61. data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
  62. data/lib/ms/parser/mzxml.rb +0 -282
  63. data/lib/ms/parser.rb +0 -108
  64. data/lib/ms/precursor.rb +0 -25
  65. data/lib/ms/scan.rb +0 -81
  66. data/lib/mspire.rb +0 -4
  67. data/lib/pi_zero.rb +0 -244
  68. data/lib/qvalue.rb +0 -161
  69. data/lib/roc.rb +0 -187
  70. data/lib/sample_enzyme.rb +0 -160
  71. data/lib/scan_i.rb +0 -21
  72. data/lib/spec_id/aa_freqs.rb +0 -170
  73. data/lib/spec_id/bioworks.rb +0 -497
  74. data/lib/spec_id/digestor.rb +0 -138
  75. data/lib/spec_id/mass.rb +0 -179
  76. data/lib/spec_id/parser/proph.rb +0 -335
  77. data/lib/spec_id/precision/filter/cmdline.rb +0 -218
  78. data/lib/spec_id/precision/filter/interactive.rb +0 -134
  79. data/lib/spec_id/precision/filter/output.rb +0 -148
  80. data/lib/spec_id/precision/filter.rb +0 -637
  81. data/lib/spec_id/precision/output.rb +0 -60
  82. data/lib/spec_id/precision/prob/cmdline.rb +0 -160
  83. data/lib/spec_id/precision/prob/output.rb +0 -94
  84. data/lib/spec_id/precision/prob.rb +0 -249
  85. data/lib/spec_id/proph/pep_summary.rb +0 -104
  86. data/lib/spec_id/proph/prot_summary.rb +0 -484
  87. data/lib/spec_id/proph.rb +0 -4
  88. data/lib/spec_id/protein_summary.rb +0 -489
  89. data/lib/spec_id/sequest/params.rb +0 -316
  90. data/lib/spec_id/sequest/pepxml.rb +0 -1458
  91. data/lib/spec_id/sequest.rb +0 -33
  92. data/lib/spec_id/sqt.rb +0 -349
  93. data/lib/spec_id/srf.rb +0 -973
  94. data/lib/spec_id.rb +0 -778
  95. data/lib/spec_id_xml.rb +0 -99
  96. data/lib/transmem/phobius.rb +0 -147
  97. data/lib/transmem/toppred.rb +0 -368
  98. data/lib/transmem.rb +0 -157
  99. data/lib/validator/aa.rb +0 -48
  100. data/lib/validator/aa_est.rb +0 -112
  101. data/lib/validator/background.rb +0 -77
  102. data/lib/validator/bias.rb +0 -95
  103. data/lib/validator/cmdline.rb +0 -431
  104. data/lib/validator/decoy.rb +0 -107
  105. data/lib/validator/digestion_based.rb +0 -70
  106. data/lib/validator/probability.rb +0 -51
  107. data/lib/validator/prot_from_pep.rb +0 -234
  108. data/lib/validator/q_value.rb +0 -32
  109. data/lib/validator/transmem.rb +0 -272
  110. data/lib/validator/true_pos.rb +0 -46
  111. data/lib/validator.rb +0 -197
  112. data/lib/xml.rb +0 -38
  113. data/lib/xml_style_parser.rb +0 -119
  114. data/lib/xmlparser_wrapper.rb +0 -19
  115. data/release_notes.txt +0 -2
  116. data/script/compile_and_plot_smriti_final.rb +0 -97
  117. data/script/create_little_pepxml.rb +0 -61
  118. data/script/degenerate_peptides.rb +0 -47
  119. data/script/estimate_fpr_by_cysteine.rb +0 -226
  120. data/script/extract_gradient_programs.rb +0 -56
  121. data/script/find_cysteine_background.rb +0 -137
  122. data/script/genuine_tps_and_probs.rb +0 -136
  123. data/script/get_apex_values_rexml.rb +0 -44
  124. data/script/histogram_probs.rb +0 -61
  125. data/script/mascot_fix_pepxml.rb +0 -123
  126. data/script/msvis.rb +0 -42
  127. data/script/mzXML2timeIndex.rb +0 -25
  128. data/script/peps_per_bin.rb +0 -67
  129. data/script/prep_dir.rb +0 -121
  130. data/script/simple_protein_digestion.rb +0 -27
  131. data/script/smriti_final_analysis.rb +0 -103
  132. data/script/sqt_to_meta.rb +0 -24
  133. data/script/top_hit_per_scan.rb +0 -67
  134. data/script/toppred_to_yaml.rb +0 -47
  135. data/script/tpp_installer.rb +0 -249
  136. data/specs/align_spec.rb +0 -79
  137. data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
  138. data/specs/bin/fasta_shaker_spec.rb +0 -259
  139. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
  140. data/specs/bin/filter_and_validate_spec.rb +0 -180
  141. data/specs/bin/ms_to_lmat_spec.rb +0 -34
  142. data/specs/bin/prob_validate_spec.rb +0 -86
  143. data/specs/bin/protein_summary_spec.rb +0 -14
  144. data/specs/fasta_spec.rb +0 -354
  145. data/specs/gi_spec.rb +0 -22
  146. data/specs/load_bin_path.rb +0 -7
  147. data/specs/merge_deep_spec.rb +0 -13
  148. data/specs/ms/gradient_program_spec.rb +0 -77
  149. data/specs/ms/msrun_spec.rb +0 -498
  150. data/specs/ms/parser_spec.rb +0 -92
  151. data/specs/ms/spectrum_spec.rb +0 -87
  152. data/specs/pi_zero_spec.rb +0 -115
  153. data/specs/qvalue_spec.rb +0 -39
  154. data/specs/roc_spec.rb +0 -251
  155. data/specs/rspec_autotest.rb +0 -149
  156. data/specs/sample_enzyme_spec.rb +0 -126
  157. data/specs/spec_helper.rb +0 -135
  158. data/specs/spec_id/aa_freqs_spec.rb +0 -52
  159. data/specs/spec_id/bioworks_spec.rb +0 -148
  160. data/specs/spec_id/digestor_spec.rb +0 -75
  161. data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
  162. data/specs/spec_id/precision/filter/output_spec.rb +0 -31
  163. data/specs/spec_id/precision/filter_spec.rb +0 -246
  164. data/specs/spec_id/precision/prob_spec.rb +0 -44
  165. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  166. data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
  167. data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
  168. data/specs/spec_id/protein_summary_spec.rb +0 -189
  169. data/specs/spec_id/sequest/params_spec.rb +0 -68
  170. data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
  171. data/specs/spec_id/sequest_spec.rb +0 -38
  172. data/specs/spec_id/sqt_spec.rb +0 -246
  173. data/specs/spec_id/srf_spec.rb +0 -172
  174. data/specs/spec_id/srf_spec_helper.rb +0 -139
  175. data/specs/spec_id_helper.rb +0 -33
  176. data/specs/spec_id_spec.rb +0 -366
  177. data/specs/spec_id_xml_spec.rb +0 -33
  178. data/specs/transmem/phobius_spec.rb +0 -425
  179. data/specs/transmem/toppred_spec.rb +0 -298
  180. data/specs/transmem_spec.rb +0 -60
  181. data/specs/transmem_spec_shared.rb +0 -64
  182. data/specs/validator/aa_est_spec.rb +0 -66
  183. data/specs/validator/aa_spec.rb +0 -40
  184. data/specs/validator/background_spec.rb +0 -67
  185. data/specs/validator/bias_spec.rb +0 -122
  186. data/specs/validator/decoy_spec.rb +0 -51
  187. data/specs/validator/fasta_helper.rb +0 -26
  188. data/specs/validator/prot_from_pep_spec.rb +0 -141
  189. data/specs/validator/transmem_spec.rb +0 -146
  190. data/specs/validator/true_pos_spec.rb +0 -58
  191. data/specs/validator_helper.rb +0 -33
  192. data/specs/xml_spec.rb +0 -12
  193. data/test_files/000_pepxml18_small.xml +0 -206
  194. data/test_files/020a.mzXML.timeIndex +0 -4710
  195. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
  196. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
  197. data/test_files/4-03-03_small-prot.xml +0 -321
  198. data/test_files/4-03-03_small.xml +0 -3876
  199. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  200. data/test_files/bioworks-3.3_10prots.xml +0 -5999
  201. data/test_files/bioworks31.params +0 -77
  202. data/test_files/bioworks32.params +0 -62
  203. data/test_files/bioworks33.params +0 -63
  204. data/test_files/bioworks_single_run_small.xml +0 -7237
  205. data/test_files/bioworks_small.fasta +0 -212
  206. data/test_files/bioworks_small.params +0 -63
  207. data/test_files/bioworks_small.phobius +0 -109
  208. data/test_files/bioworks_small.toppred.out +0 -2847
  209. data/test_files/bioworks_small.xml +0 -5610
  210. data/test_files/bioworks_with_INV_small.xml +0 -3753
  211. data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
  212. data/test_files/corrupted_900.srf +0 -0
  213. data/test_files/head_of_7MIX.srf +0 -0
  214. data/test_files/interact-opd1_mods_small-prot.xml +0 -304
  215. data/test_files/messups.fasta +0 -297
  216. data/test_files/opd1/000.my_answer.100lines.xml +0 -101
  217. data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
  218. data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
  219. data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
  220. data/test_files/opd1/000_020-prot.png +0 -0
  221. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
  222. data/test_files/opd1/000_020_3prots-prot.xml +0 -62
  223. data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
  224. data/test_files/opd1/sequest.3.1.params +0 -77
  225. data/test_files/opd1/sequest.3.2.params +0 -62
  226. data/test_files/opd1/twenty_scans.mzXML +0 -418
  227. data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
  228. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  229. data/test_files/opd1/twenty_scans_answ.lmata +0 -9
  230. data/test_files/opd1_020_beginning.RAW +0 -0
  231. data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
  232. data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
  233. data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
  234. data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
  235. data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
  236. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
  237. data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
  238. data/test_files/pepproph_small.xml +0 -4691
  239. data/test_files/phobius.small.noheader.txt +0 -50
  240. data/test_files/phobius.small.small.txt +0 -53
  241. data/test_files/s01_anC1_ld020mM.key.txt +0 -25
  242. data/test_files/s01_anC1_ld020mM.meth +0 -0
  243. data/test_files/small.fasta +0 -297
  244. data/test_files/small.sqt +0 -87
  245. data/test_files/smallraw.RAW +0 -0
  246. data/test_files/tf_bioworks2excel.bioXML +0 -14340
  247. data/test_files/tf_bioworks2excel.txt.actual +0 -1035
  248. data/test_files/toppred.small.out +0 -416
  249. data/test_files/toppred.xml.out +0 -318
  250. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
  251. data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
  252. data/test_files/yeast_gly_small-prot.xml +0 -265
  253. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
  254. data/test_files/yeast_gly_small.xml +0 -3807
  255. data/test_files/yeast_gly_small2.parentTimes +0 -6
data/test_files/corrupted_900.srf DELETED
Binary file
data/test_files/head_of_7MIX.srf DELETED
Binary file
data/test_files/interact-opd1_mods_small-prot.xml DELETED
@@ -1,304 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
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- <?xml-stylesheet type="text/xsl" href="/work/tpp-data/interact-opd1_mods-prot.xsl"?>
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- <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>