mspire 0.4.9 → 0.5.0

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 (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
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data/test_files/interact-opd1_mods_small-prot.xml DELETED
@@ -1,304 +0,0 @@
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>