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/bioworks_with_SHUFF_small.xml DELETED
@@ -1,2503 +0,0 @@
1
- <?xml version="1.0"?>
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- <sequestresults xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="schema1.xsd">
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- <bioworksinfo>3.2 EF1</bioworksinfo>
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- <protein>
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- <reference>gi|114939|sp|P00722|BGAL_ECOLI Beta-galactosidase (Lactase)</reference>
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- <protein_probability>2.03E-8</protein_probability>
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- <consensus_score>178.2</consensus_score>
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- <Sf>0.00</Sf>
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- <unified_score>0</unified_score>
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- <coverage>0.0</coverage>
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- <pI>0.0</pI>
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- <weight>116482.1</weight>
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- <accession>114939</accession>
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- <peptide>
15
- <file>7MIX_STD_110802_1, 386</file>
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- <sequence>R.SLNGEWR.F</sequence>
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- <mass>861.92</mass>
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- <deltamass>0.14</deltamass>
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- <charge>2</charge>
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- <peptide_probability>2.03E-8</peptide_probability>
21
- <xcorr>1.351</xcorr>
22
- <deltacn>0.146</deltacn>
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- <sp>190.9</sp>
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- <rsp>14</rsp>
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- <ions>6/12</ions>
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- <count>1</count>
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- <tic>0</tic>
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- </peptide>
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- <peptide>
30
- <file>7MIX_STD_110802_1, 389</file>
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- <sequence>R.SLNGEWR.F</sequence>
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- <mass>861.92</mass>
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- <deltamass>0.08</deltamass>
34
- <charge>2</charge>
35
- <peptide_probability>2.03E-8</peptide_probability>
36
- <xcorr>1.492</xcorr>
37
- <deltacn>0.152</deltacn>
38
- <sp>316.1</sp>
39
- <rsp>1</rsp>
40
- <ions>8/12</ions>
41
- <count>1</count>
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- <tic>0</tic>
43
- </peptide>
44
- <peptide>
45
- <file>7MIX_STD_110802_1, 462</file>
46
- <sequence>R.WVGYGQDSR.L</sequence>
47
- <mass>1068.12</mass>
48
- <deltamass>0.96</deltamass>
49
- <charge>2</charge>
50
- <peptide_probability>2.03E-8</peptide_probability>
51
- <xcorr>1.985</xcorr>
52
- <deltacn>0.321</deltacn>
53
- <sp>690.6</sp>
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- <rsp>1</rsp>
55
- <ions>13/16</ions>
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- <count>1</count>
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- <tic>0</tic>
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- </peptide>
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- <peptide>
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- <file>7MIX_STD_110802_1, 471</file>
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- <sequence>R.WVGYGQDSR.L</sequence>
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- <mass>1068.12</mass>
63
- <deltamass>0.94</deltamass>
64
- <charge>2</charge>
65
- <peptide_probability>2.03E-8</peptide_probability>
66
- <xcorr>2.577</xcorr>
67
- <deltacn>0.262</deltacn>
68
- <sp>955.8</sp>
69
- <rsp>1</rsp>
70
- <ions>15/16</ions>
71
- <count>1</count>
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- <tic>0</tic>
73
- </peptide>
74
- <peptide>
75
- <file>7MIX_STD_110802_1, 855</file>
76
- <sequence>R.YSQQQLMETSHR.H</sequence>
77
- <mass>1508.64</mass>
78
- <deltamass>0.64</deltamass>
79
- <charge>3</charge>
80
- <peptide_probability>2.03E-8</peptide_probability>
81
- <xcorr>2.392</xcorr>
82
- <deltacn>0.216</deltacn>
83
- <sp>766.7</sp>
84
- <rsp>1</rsp>
85
- <ions>19/44</ions>
86
- <count>1</count>
87
- <tic>0</tic>
88
- </peptide>
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- <peptide>
90
- <file>7MIX_STD_110802_1, 1368</file>
91
- <sequence>R.APLDNDIGVSEATR.I</sequence>
92
- <mass>1458.56</mass>
93
- <deltamass>0.55</deltamass>
94
- <charge>2</charge>
95
- <peptide_probability>2.03E-8</peptide_probability>
96
- <xcorr>3.703</xcorr>
97
- <deltacn>0.532</deltacn>
98
- <sp>1376.1</sp>
99
- <rsp>1</rsp>
100
- <ions>18/26</ions>
101
- <count>1</count>
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- <tic>0</tic>
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- </peptide>
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- <peptide>
105
- <file>7MIX_STD_110802_1, 1373</file>
106
- <sequence>R.APLDNDIGVSEATR.I</sequence>
107
- <mass>1458.56</mass>
108
- <deltamass>0.29</deltamass>
109
- <charge>2</charge>
110
- <peptide_probability>2.03E-8</peptide_probability>
111
- <xcorr>3.499</xcorr>
112
- <deltacn>0.376</deltacn>
113
- <sp>1075.1</sp>
114
- <rsp>1</rsp>
115
- <ions>17/26</ions>
116
- <count>1</count>
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- <tic>0</tic>
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- </peptide>
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- <peptide>
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- <file>7MIX_STD_110802_1, 1443</file>
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- <sequence>K.YWQAFR.Q</sequence>
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- <mass>870.98</mass>
123
- <deltamass>0.26</deltamass>
124
- <charge>2</charge>
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- <peptide_probability>2.03E-8</peptide_probability>
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- <xcorr>1.699</xcorr>
127
- <deltacn>0.086</deltacn>
128
- <sp>357.0</sp>
129
- <rsp>1</rsp>
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- <ions>8/10</ions>
131
- <count>1</count>
132
- <tic>0</tic>
133
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627
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628
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629
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630
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631
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632
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633
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634
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635
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636
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637
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641
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650
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651
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656
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663
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665
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666
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669
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716
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723
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730
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731
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742
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745
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746
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776
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786
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789
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791
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836
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1097
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1102
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1104
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1105
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1106
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1107
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1108
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1109
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1110
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1111
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1112
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1113
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1114
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1115
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1116
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1117
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1118
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1119
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1120
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1121
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1122
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1123
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1124
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1125
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1126
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1127
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1128
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1129
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1130
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1131
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1132
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1133
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1134
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1135
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1136
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1137
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1138
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1139
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1140
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1141
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1142
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1143
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1144
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1145
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1146
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1147
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1148
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1149
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1150
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1151
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1152
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1153
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1154
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1155
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1156
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1157
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1158
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1159
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1160
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1161
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1162
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1163
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1164
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1165
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1166
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1167
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1168
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1169
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1170
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1171
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1172
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1173
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1174
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1175
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1176
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1177
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1178
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1179
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1180
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1181
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1182
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1183
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1184
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1185
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1186
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1187
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1188
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1189
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1190
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1191
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1192
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1193
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1194
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1195
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1196
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1197
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1198
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1199
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1200
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1201
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1202
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1203
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1204
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1205
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1206
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1207
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1208
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1209
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1210
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1211
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1212
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1213
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1214
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1215
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1216
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1217
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1218
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1219
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1220
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1221
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1222
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1223
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1224
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1225
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1226
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1227
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1228
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1229
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1230
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1231
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1232
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1233
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1234
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1235
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1236
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1237
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1238
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1239
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1240
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1241
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1242
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1243
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1244
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1245
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1246
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1247
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1248
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1249
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1250
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1251
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1252
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1253
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1254
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1255
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1256
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1257
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1258
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1259
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1260
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1261
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1262
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1263
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1264
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1265
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1266
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1267
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1268
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1269
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1270
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1271
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1272
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1273
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1274
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1275
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1276
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1277
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1278
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1279
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1280
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1281
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1282
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1283
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1284
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1285
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1286
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1287
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1289
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1291
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1292
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1293
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1294
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1295
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1296
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1297
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1298
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1299
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1300
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1301
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1302
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1304
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1306
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1307
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1308
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1309
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1310
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1311
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1312
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1313
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1314
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1315
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1316
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1317
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1319
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1320
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1321
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1322
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1323
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1324
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1325
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1326
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1327
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1328
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1329
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1330
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1331
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1332
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1333
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1334
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1335
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1336
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1337
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1338
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1339
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1340
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1341
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1342
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1343
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1345
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1349
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1350
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1351
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1352
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1354
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1355
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1357
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1360
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1361
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1362
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1364
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1366
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1367
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1368
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1369
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1370
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1371
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1372
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1379
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1382
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1384
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1386
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1387
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1396
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1397
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1398
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1399
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1400
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1401
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1402
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1403
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1404
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1405
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1406
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1407
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1409
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1410
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1412
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1418
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1420
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1421
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1422
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1423
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1424
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1425
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1426
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1427
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1428
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1430
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1431
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1432
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1433
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1434
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1435
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1436
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1437
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1438
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1439
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1440
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1441
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1447
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1454
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1462
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1483
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1499
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1501
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1507
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1510
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1513
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1514
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1515
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1516
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1520
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1521
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1522
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1523
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1524
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1525
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1526
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1538
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1539
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1540
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1541
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1542
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1548
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1551
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1552
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1554
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1555
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1557
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1561
- <mass>1403.54</mass>
1562
- <deltamass>0.09</deltamass>
1563
- <charge>2</charge>
1564
- <peptide_probability>6.16E-6</peptide_probability>
1565
- <xcorr>3.246</xcorr>
1566
- <deltacn>0.395</deltacn>
1567
- <sp>551.2</sp>
1568
- <rsp>1</rsp>
1569
- <ions>16/24</ions>
1570
- <count>1</count>
1571
- <tic>4406</tic>
1572
- </peptide>
1573
- <peptide>
1574
- <file>7MIX_STD_110802_1, 747</file>
1575
- <sequence>K.VLGNPSNEEMNAK.K</sequence>
1576
- <mass>1403.54</mass>
1577
- <deltamass>0.38</deltamass>
1578
- <charge>2</charge>
1579
- <peptide_probability>6.16E-6</peptide_probability>
1580
- <xcorr>3.300</xcorr>
1581
- <deltacn>0.430</deltacn>
1582
- <sp>525.6</sp>
1583
- <rsp>1</rsp>
1584
- <ions>15/24</ions>
1585
- <count>1</count>
1586
- <tic>4407</tic>
1587
- </peptide>
1588
- <peptide>
1589
- <file>7MIX_STD_110802_1, 2573</file>
1590
- <sequence>K.ITLSQVGDVLR.A</sequence>
1591
- <mass>1201.40</mass>
1592
- <deltamass>0.32</deltamass>
1593
- <charge>2</charge>
1594
- <peptide_probability>6.16E-6</peptide_probability>
1595
- <xcorr>3.751</xcorr>
1596
- <deltacn>0.455</deltacn>
1597
- <sp>1533.5</sp>
1598
- <rsp>1</rsp>
1599
- <ions>18/20</ions>
1600
- <count>3</count>
1601
- <tic>6711</tic>
1602
- </peptide>
1603
- <peptide>
1604
- <file>7MIX_STD_110802_1, 2582</file>
1605
- <sequence>K.ITLSQVGDVLR.A</sequence>
1606
- <mass>1201.40</mass>
1607
- <deltamass>1.03</deltamass>
1608
- <charge>2</charge>
1609
- <peptide_probability>6.16E-6</peptide_probability>
1610
- <xcorr>3.504</xcorr>
1611
- <deltacn>0.327</deltacn>
1612
- <sp>1392.3</sp>
1613
- <rsp>1</rsp>
1614
- <ions>17/20</ions>
1615
- <count>3</count>
1616
- <tic>8068</tic>
1617
- </peptide>
1618
- <peptide>
1619
- <file>7MIX_STD_110802_1, 3003</file>
1620
- <sequence>K.KVLGNPSNEEMNAKK.I</sequence>
1621
- <mass>1659.89</mass>
1622
- <deltamass>0.69</deltamass>
1623
- <charge>2</charge>
1624
- <peptide_probability>6.16E-6</peptide_probability>
1625
- <xcorr>0.826</xcorr>
1626
- <deltacn>0.070</deltacn>
1627
- <sp>71.1</sp>
1628
- <rsp>63</rsp>
1629
- <ions>6/28</ions>
1630
- <count>1</count>
1631
- <tic>5897</tic>
1632
- </peptide>
1633
- </protein>
1634
- <protein>
1635
- <reference>SHUFF_gi|20541352|ref|XP_047672.4| similar to KIAA1673 protein [Homo sapiens]</reference>
1636
- <protein_probability>2.50E-5</protein_probability>
1637
- <consensus_score>16.1</consensus_score>
1638
- <Sf>0.00</Sf>
1639
- <unified_score>0</unified_score>
1640
- <coverage>0.0</coverage>
1641
- <pI>0.0</pI>
1642
- <weight>78313.5</weight>
1643
- <accession>0</accession>
1644
- <peptide>
1645
- <file>7MIX_STD_110802_1, 1739</file>
1646
- <sequence>R.LPWSGFINLPRNAER.L</sequence>
1647
- <mass>1771.02</mass>
1648
- <deltamass>0.35</deltamass>
1649
- <charge>3</charge>
1650
- <peptide_probability>2.50E-5</peptide_probability>
1651
- <xcorr>1.796</xcorr>
1652
- <deltacn>0.491</deltacn>
1653
- <sp>419.2</sp>
1654
- <rsp>4</rsp>
1655
- <ions>18/56</ions>
1656
- <count>0</count>
1657
- <tic>7222</tic>
1658
- </peptide>
1659
- <peptide>
1660
- <file>7MIX_STD_110802_1, 2780</file>
1661
- <sequence>K.FLNSLGGSFAPFAQK.V</sequence>
1662
- <mass>1584.80</mass>
1663
- <deltamass>0.87</deltamass>
1664
- <charge>2</charge>
1665
- <peptide_probability>2.50E-5</peptide_probability>
1666
- <xcorr>1.046</xcorr>
1667
- <deltacn>0.058</deltacn>
1668
- <sp>155.6</sp>
1669
- <rsp>10</rsp>
1670
- <ions>8/28</ions>
1671
- <count>0</count>
1672
- <tic>7154</tic>
1673
- </peptide>
1674
- </protein>
1675
- <protein>
1676
- <reference>gi|29739414|ref|XP_294015.1| similar to Glyceraldehyde 3-phosphate dehydrogenase, liver (GAPDH) [Ho</reference>
1677
- <protein_probability>3.02E-5</protein_probability>
1678
- <consensus_score>18.2</consensus_score>
1679
- <Sf>0.00</Sf>
1680
- <unified_score>0</unified_score>
1681
- <coverage>0.0</coverage>
1682
- <pI>0.0</pI>
1683
- <weight>26916.7</weight>
1684
- <accession>29739414</accession>
1685
- <peptide>
1686
- <file>7MIX_STD_110802_1, 2628 - 2630</file>
1687
- <sequence>K.LISWYDNEFGYSNR.V</sequence>
1688
- <mass>1764.87</mass>
1689
- <deltamass>0.77</deltamass>
1690
- <charge>2</charge>
1691
- <peptide_probability>3.02E-5</peptide_probability>
1692
- <xcorr>3.978</xcorr>
1693
- <deltacn>0.510</deltacn>
1694
- <sp>1722.1</sp>
1695
- <rsp>1</rsp>
1696
- <ions>19/26</ions>
1697
- <count>0</count>
1698
- <tic>9970</tic>
1699
- </peptide>
1700
- <peptide>
1701
- <file>7MIX_STD_110802_1, 1838</file>
1702
- <sequence>K.YYDIKKMMK.Q</sequence>
1703
- <mass>1220.53</mass>
1704
- <deltamass>1.31</deltamass>
1705
- <charge>1</charge>
1706
- <peptide_probability>3.02E-5</peptide_probability>
1707
- <xcorr>1.142</xcorr>
1708
- <deltacn>0.283</deltacn>
1709
- <sp>239.8</sp>
1710
- <rsp>3</rsp>
1711
- <ions>9/16</ions>
1712
- <count>0</count>
1713
- <tic>6308</tic>
1714
- </peptide>
1715
- </protein>
1716
- <protein>
1717
- <reference>SHUFF_gi|14550409|ref|NP_000491.2| cytochrome P450, family 21, subfamily A, polypeptide 2; steroid</reference>
1718
- <protein_probability>3.14E-5</protein_probability>
1719
- <consensus_score>18.1</consensus_score>
1720
- <Sf>0.00</Sf>
1721
- <unified_score>0</unified_score>
1722
- <coverage>0.0</coverage>
1723
- <pI>0.0</pI>
1724
- <weight>56001.2</weight>
1725
- <accession>0</accession>
1726
- <peptide>
1727
- <file>7MIX_STD_110802_1, 3386</file>
1728
- <sequence>K.WAPLDEILEMNLIPMLVKNK.A</sequence>
1729
- <mass>2368.89</mass>
1730
- <deltamass>0.14</deltamass>
1731
- <charge>2</charge>
1732
- <peptide_probability>3.14E-5</peptide_probability>
1733
- <xcorr>2.813</xcorr>
1734
- <deltacn>0.012</deltacn>
1735
- <sp>298.7</sp>
1736
- <rsp>2</rsp>
1737
- <ions>11/38</ions>
1738
- <count>0</count>
1739
- <tic>9440</tic>
1740
- </peptide>
1741
- <peptide>
1742
- <file>7MIX_STD_110802_1, 3381</file>
1743
- <sequence>K.WAPLDEILEMNLIPMLVKNK.A</sequence>
1744
- <mass>2368.89</mass>
1745
- <deltamass>0.12</deltamass>
1746
- <charge>2</charge>
1747
- <peptide_probability>3.14E-5</peptide_probability>
1748
- <xcorr>2.256</xcorr>
1749
- <deltacn>0.027</deltacn>
1750
- <sp>320.8</sp>
1751
- <rsp>12</rsp>
1752
- <ions>11/38</ions>
1753
- <count>0</count>
1754
- <tic>10788</tic>
1755
- </peptide>
1756
- <peptide>
1757
- <file>7MIX_STD_110802_1, 5090</file>
1758
- <sequence>R.IMAPWVFILMTEEWTPK.A</sequence>
1759
- <mass>2093.54</mass>
1760
- <deltamass>1.28</deltamass>
1761
- <charge>2</charge>
1762
- <peptide_probability>3.14E-5</peptide_probability>
1763
- <xcorr>0.538</xcorr>
1764
- <deltacn>0.377</deltacn>
1765
- <sp>18.2</sp>
1766
- <rsp>125</rsp>
1767
- <ions>4/32</ions>
1768
- <count>0</count>
1769
- <tic>3576</tic>
1770
- </peptide>
1771
- <peptide>
1772
- <file>7MIX_STD_110802_1, 3387</file>
1773
- <sequence>K.WAPLDEILEMNLIPMLVKNK.A</sequence>
1774
- <mass>2368.89</mass>
1775
- <deltamass>0.11</deltamass>
1776
- <charge>3</charge>
1777
- <peptide_probability>3.14E-5</peptide_probability>
1778
- <xcorr>2.872</xcorr>
1779
- <deltacn>0.150</deltacn>
1780
- <sp>1074.8</sp>
1781
- <rsp>2</rsp>
1782
- <ions>26/76</ions>
1783
- <count>0</count>
1784
- <tic>9563</tic>
1785
- </peptide>
1786
- </protein>
1787
- <protein>
1788
- <reference>gi|1786543|gb|AAC73450.1| 3-(3-hydroxyphenyl)propionate hydroxylase [Escherichia coli K12]</reference>
1789
- <protein_probability>8.63E-5</protein_probability>
1790
- <consensus_score>18.1</consensus_score>
1791
- <Sf>0.00</Sf>
1792
- <unified_score>0</unified_score>
1793
- <coverage>0.0</coverage>
1794
- <pI>0.0</pI>
1795
- <weight>62185.3</weight>
1796
- <accession>1786543</accession>
1797
- <peptide>
1798
- <file>7MIX_STD_110802_1, 902</file>
1799
- <sequence>K.VLPNPDNVELIR.Q</sequence>
1800
- <mass>1379.59</mass>
1801
- <deltamass>1.22</deltamass>
1802
- <charge>3</charge>
1803
- <peptide_probability>8.63E-5</peptide_probability>
1804
- <xcorr>1.742</xcorr>
1805
- <deltacn>0.229</deltacn>
1806
- <sp>408.4</sp>
1807
- <rsp>2</rsp>
1808
- <ions>16/44</ions>
1809
- <count>0</count>
1810
- <tic>4697</tic>
1811
- </peptide>
1812
- <peptide>
1813
- <file>7MIX_STD_110802_1, 4428</file>
1814
- <sequence>R.ALGTR.F</sequence>
1815
- <mass>517.60</mass>
1816
- <deltamass>1.33</deltamass>
1817
- <charge>1</charge>
1818
- <peptide_probability>8.63E-5</peptide_probability>
1819
- <xcorr>0.606</xcorr>
1820
- <deltacn>0.095</deltacn>
1821
- <sp>30.7</sp>
1822
- <rsp>24</rsp>
1823
- <ions>4/8</ions>
1824
- <count>2</count>
1825
- <tic>2762</tic>
1826
- </peptide>
1827
- </protein>
1828
- <protein>
1829
- <reference>gi|1790518|gb|AAD13464.1| putative enzyme [Escherichia coli K12]</reference>
1830
- <protein_probability>1.12E-4</protein_probability>
1831
- <consensus_score>10.1</consensus_score>
1832
- <Sf>0.00</Sf>
1833
- <unified_score>0</unified_score>
1834
- <coverage>0.0</coverage>
1835
- <pI>0.0</pI>
1836
- <weight>70869.1</weight>
1837
- <accession>1790518</accession>
1838
- <peptide>
1839
- <file>7MIX_STD_110802_1, 4434</file>
1840
- <sequence>K.WSYGEPLIRLIIAGPILMGCMFLMR.T</sequence>
1841
- <mass>2882.61</mass>
1842
- <deltamass>0.06</deltamass>
1843
- <charge>2</charge>
1844
- <peptide_probability>1.12E-4</peptide_probability>
1845
- <xcorr>1.054</xcorr>
1846
- <deltacn>0.240</deltacn>
1847
- <sp>145.4</sp>
1848
- <rsp>1</rsp>
1849
- <ions>10/48</ions>
1850
- <count>0</count>
1851
- <tic>4570</tic>
1852
- </peptide>
1853
- </protein>
1854
- <protein>
1855
- <reference>SHUFF_gi|1787063|gb|AAC73927.1| transcriptional repressor for deo operon, tsx, nupG [Escherichia co</reference>
1856
- <protein_probability>1.23E-4</protein_probability>
1857
- <consensus_score>16.1</consensus_score>
1858
- <Sf>0.00</Sf>
1859
- <unified_score>0</unified_score>
1860
- <coverage>0.0</coverage>
1861
- <pI>0.0</pI>
1862
- <weight>28547.8</weight>
1863
- <accession>0</accession>
1864
- <peptide>
1865
- <file>7MIX_STD_110802_1, 1668</file>
1866
- <sequence>R.IQVDLEDALR.A</sequence>
1867
- <mass>1172.31</mass>
1868
- <deltamass>0.83</deltamass>
1869
- <charge>2</charge>
1870
- <peptide_probability>1.23E-4</peptide_probability>
1871
- <xcorr>0.970</xcorr>
1872
- <deltacn>0.034</deltacn>
1873
- <sp>214.7</sp>
1874
- <rsp>39</rsp>
1875
- <ions>8/18</ions>
1876
- <count>0</count>
1877
- <tic>8711</tic>
1878
- </peptide>
1879
- <peptide>
1880
- <file>7MIX_STD_110802_1, 3083</file>
1881
- <sequence>K.VVDSYEDPIFIRPNRLFR.K</sequence>
1882
- <mass>2237.55</mass>
1883
- <deltamass>0.87</deltamass>
1884
- <charge>3</charge>
1885
- <peptide_probability>1.23E-4</peptide_probability>
1886
- <xcorr>1.552</xcorr>
1887
- <deltacn>0.080</deltacn>
1888
- <sp>439.7</sp>
1889
- <rsp>2</rsp>
1890
- <ions>18/68</ions>
1891
- <count>0</count>
1892
- <tic>11703</tic>
1893
- </peptide>
1894
- </protein>
1895
- <protein>
1896
- <reference>SHUFF_gi|30147010|ref|XP_303064.1| hypothetical protein XP_303064 [Homo sapiens]</reference>
1897
- <protein_probability>1.26E-4</protein_probability>
1898
- <consensus_score>10.0</consensus_score>
1899
- <Sf>0.00</Sf>
1900
- <unified_score>0</unified_score>
1901
- <coverage>0.0</coverage>
1902
- <pI>0.0</pI>
1903
- <weight>13349.3</weight>
1904
- <accession>0</accession>
1905
- <peptide>
1906
- <file>7MIX_STD_110802_1, 4608</file>
1907
- <sequence>K.RRPKTLTVASMQVHR.V</sequence>
1908
- <mass>1781.12</mass>
1909
- <deltamass>1.07</deltamass>
1910
- <charge>2</charge>
1911
- <peptide_probability>1.26E-4</peptide_probability>
1912
- <xcorr>0.850</xcorr>
1913
- <deltacn>0.080</deltacn>
1914
- <sp>87.7</sp>
1915
- <rsp>1</rsp>
1916
- <ions>7/28</ions>
1917
- <count>0</count>
1918
- <tic>3777</tic>
1919
- </peptide>
1920
- </protein>
1921
- <protein>
1922
- <reference>SHUFF_gi|21265052|ref|NP_542453.2| a disintegrin-like and metalloprotease (reprolysin type) with th</reference>
1923
- <protein_probability>1.43E-4</protein_probability>
1924
- <consensus_score>8.1</consensus_score>
1925
- <Sf>0.00</Sf>
1926
- <unified_score>0</unified_score>
1927
- <coverage>0.0</coverage>
1928
- <pI>0.0</pI>
1929
- <weight>133887.5</weight>
1930
- <accession>0</accession>
1931
- <peptide>
1932
- <file>7MIX_STD_110802_1, 2076</file>
1933
- <sequence>K.FKGRDHDGGPEK.A</sequence>
1934
- <mass>1343.43</mass>
1935
- <deltamass>0.70</deltamass>
1936
- <charge>2</charge>
1937
- <peptide_probability>1.43E-4</peptide_probability>
1938
- <xcorr>1.293</xcorr>
1939
- <deltacn>0.179</deltacn>
1940
- <sp>354.4</sp>
1941
- <rsp>1</rsp>
1942
- <ions>13/22</ions>
1943
- <count>0</count>
1944
- <tic>3496</tic>
1945
- </peptide>
1946
- </protein>
1947
- <protein>
1948
- <reference>gi|1789467|gb|AAC76120.1| orf, hypothetical protein [Escherichia coli K12]</reference>
1949
- <protein_probability>1.56E-4</protein_probability>
1950
- <consensus_score>10.1</consensus_score>
1951
- <Sf>0.00</Sf>
1952
- <unified_score>0</unified_score>
1953
- <coverage>0.0</coverage>
1954
- <pI>0.0</pI>
1955
- <weight>20883.1</weight>
1956
- <accession>1789467</accession>
1957
- <peptide>
1958
- <file>7MIX_STD_110802_1, 4154</file>
1959
- <sequence>R.NAPPINKVMYDNKIHVLK.N</sequence>
1960
- <mass>2095.50</mass>
1961
- <deltamass>0.54</deltamass>
1962
- <charge>2</charge>
1963
- <peptide_probability>1.56E-4</peptide_probability>
1964
- <xcorr>1.769</xcorr>
1965
- <deltacn>0.202</deltacn>
1966
- <sp>316.7</sp>
1967
- <rsp>7</rsp>
1968
- <ions>12/34</ions>
1969
- <count>0</count>
1970
- <tic>8330</tic>
1971
- </peptide>
1972
- <peptide>
1973
- <file>7MIX_STD_110802_1, 1409</file>
1974
- <sequence>K.NALGLHTAVSRVQGGK.L</sequence>
1975
- <mass>1608.83</mass>
1976
- <deltamass>0.16</deltamass>
1977
- <charge>3</charge>
1978
- <peptide_probability>1.56E-4</peptide_probability>
1979
- <xcorr>1.364</xcorr>
1980
- <deltacn>0.086</deltacn>
1981
- <sp>154.9</sp>
1982
- <rsp>101</rsp>
1983
- <ions>14/60</ions>
1984
- <count>0</count>
1985
- <tic>4610</tic>
1986
- </peptide>
1987
- </protein>
1988
- <protein>
1989
- <reference>SHUFF_gi|29893808|ref|NP_536356.3| actin-related protein M2; actin-related protein hArpM2; actin-re</reference>
1990
- <protein_probability>1.91E-4</protein_probability>
1991
- <consensus_score>20.1</consensus_score>
1992
- <Sf>0.00</Sf>
1993
- <unified_score>0</unified_score>
1994
- <coverage>0.0</coverage>
1995
- <pI>0.0</pI>
1996
- <weight>41701.5</weight>
1997
- <accession>0</accession>
1998
- <peptide>
1999
- <file>7MIX_STD_110802_1, 1731</file>
2000
- <sequence>R.YEYLKK.V</sequence>
2001
- <mass>843.99</mass>
2002
- <deltamass>0.81</deltamass>
2003
- <charge>1</charge>
2004
- <peptide_probability>1.91E-4</peptide_probability>
2005
- <xcorr>1.127</xcorr>
2006
- <deltacn>0.063</deltacn>
2007
- <sp>374.6</sp>
2008
- <rsp>1</rsp>
2009
- <ions>8/10</ions>
2010
- <count>0</count>
2011
- <tic>4017</tic>
2012
- </peptide>
2013
- <peptide>
2014
- <file>7MIX_STD_110802_1, 3663</file>
2015
- <sequence>K.IDSEGADCELSDYSAPRGK.K</sequence>
2016
- <mass>2014.12</mass>
2017
- <deltamass>0.88</deltamass>
2018
- <charge>3</charge>
2019
- <peptide_probability>1.91E-4</peptide_probability>
2020
- <xcorr>1.522</xcorr>
2021
- <deltacn>0.301</deltacn>
2022
- <sp>795.7</sp>
2023
- <rsp>3</rsp>
2024
- <ions>21/72</ions>
2025
- <count>0</count>
2026
- <tic>12215</tic>
2027
- </peptide>
2028
- <peptide>
2029
- <file>7MIX_STD_110802_1, 1515</file>
2030
- <sequence>R.DITVIDNQAK.A</sequence>
2031
- <mass>1117.23</mass>
2032
- <deltamass>1.39</deltamass>
2033
- <charge>1</charge>
2034
- <peptide_probability>1.91E-4</peptide_probability>
2035
- <xcorr>1.225</xcorr>
2036
- <deltacn>0.174</deltacn>
2037
- <sp>149.2</sp>
2038
- <rsp>98</rsp>
2039
- <ions>7/18</ions>
2040
- <count>0</count>
2041
- <tic>5429</tic>
2042
- </peptide>
2043
- </protein>
2044
- <protein>
2045
- <reference>SHUFF_gi|17149805|ref|NP_476505.1| alpha 3 type VI collagen isoform 2 precursor; collagen VI, alpha</reference>
2046
- <protein_probability>2.19E-4</protein_probability>
2047
- <consensus_score>36.1</consensus_score>
2048
- <Sf>0.00</Sf>
2049
- <unified_score>0</unified_score>
2050
- <coverage>0.0</coverage>
2051
- <pI>0.0</pI>
2052
- <weight>325174.1</weight>
2053
- <accession>0</accession>
2054
- <peptide>
2055
- <file>7MIX_STD_110802_1, 5468</file>
2056
- <sequence>K.NNAFPIRDLHSSAFPQINTQDTIFGRYNPLTNR.V</sequence>
2057
- <mass>3820.19</mass>
2058
- <deltamass>1.20</deltamass>
2059
- <charge>3</charge>
2060
- <peptide_probability>2.19E-4</peptide_probability>
2061
- <xcorr>1.074</xcorr>
2062
- <deltacn>0.021</deltacn>
2063
- <sp>174.1</sp>
2064
- <rsp>10</rsp>
2065
- <ions>19/128</ions>
2066
- <count>0</count>
2067
- <tic>9788</tic>
2068
- </peptide>
2069
- <peptide>
2070
- <file>7MIX_STD_110802_1, 2315</file>
2071
- <sequence>K.QAPPLFAYSFEKVLK.Y</sequence>
2072
- <mass>1739.05</mass>
2073
- <deltamass>0.07</deltamass>
2074
- <charge>2</charge>
2075
- <peptide_probability>2.19E-4</peptide_probability>
2076
- <xcorr>1.240</xcorr>
2077
- <deltacn>0.233</deltacn>
2078
- <sp>134.2</sp>
2079
- <rsp>52</rsp>
2080
- <ions>8/28</ions>
2081
- <count>0</count>
2082
- <tic>8668</tic>
2083
- </peptide>
2084
- <peptide>
2085
- <file>7MIX_STD_110802_1, 2655</file>
2086
- <sequence>K.VLKYGLFAERGK.R</sequence>
2087
- <mass>1381.65</mass>
2088
- <deltamass>0.88</deltamass>
2089
- <charge>2</charge>
2090
- <peptide_probability>2.19E-4</peptide_probability>
2091
- <xcorr>1.678</xcorr>
2092
- <deltacn>0.087</deltacn>
2093
- <sp>504.5</sp>
2094
- <rsp>3</rsp>
2095
- <ions>11/22</ions>
2096
- <count>0</count>
2097
- <tic>9664</tic>
2098
- </peptide>
2099
- <peptide>
2100
- <file>7MIX_STD_110802_1, 3767</file>
2101
- <sequence>R.VLLIVDHARPEDGAALLGELYR.L</sequence>
2102
- <mass>2421.78</mass>
2103
- <deltamass>0.57</deltamass>
2104
- <charge>2</charge>
2105
- <peptide_probability>2.19E-4</peptide_probability>
2106
- <xcorr>1.102</xcorr>
2107
- <deltacn>0.212</deltacn>
2108
- <sp>152.9</sp>
2109
- <rsp>2</rsp>
2110
- <ions>13/42</ions>
2111
- <count>0</count>
2112
- <tic>5646</tic>
2113
- </peptide>
2114
- <peptide>
2115
- <file>7MIX_STD_110802_1, 5856</file>
2116
- <sequence>R.GIVPDPVTVLDTSFILRAIAIK.I</sequence>
2117
- <mass>2339.80</mass>
2118
- <deltamass>0.37</deltamass>
2119
- <charge>3</charge>
2120
- <peptide_probability>2.19E-4</peptide_probability>
2121
- <xcorr>1.201</xcorr>
2122
- <deltacn>0.144</deltacn>
2123
- <sp>117.6</sp>
2124
- <rsp>39</rsp>
2125
- <ions>15/84</ions>
2126
- <count>0</count>
2127
- <tic>4211</tic>
2128
- </peptide>
2129
- <peptide>
2130
- <file>7MIX_STD_110802_1, 6518</file>
2131
- <sequence>R.YLHGEPLHEVPVEPPSPGNR.I</sequence>
2132
- <mass>2225.45</mass>
2133
- <deltamass>1.02</deltamass>
2134
- <charge>3</charge>
2135
- <peptide_probability>2.19E-4</peptide_probability>
2136
- <xcorr>0.940</xcorr>
2137
- <deltacn>0.125</deltacn>
2138
- <sp>36.2</sp>
2139
- <rsp>205</rsp>
2140
- <ions>7/76</ions>
2141
- <count>0</count>
2142
- <tic>3907</tic>
2143
- </peptide>
2144
- <peptide>
2145
- <file>7MIX_STD_110802_1, 2696</file>
2146
- <sequence>K.EGIGR.V</sequence>
2147
- <mass>531.58</mass>
2148
- <deltamass>0.66</deltamass>
2149
- <charge>1</charge>
2150
- <peptide_probability>2.19E-4</peptide_probability>
2151
- <xcorr>0.764</xcorr>
2152
- <deltacn>1.100</deltacn>
2153
- <sp>167.1</sp>
2154
- <rsp>2</rsp>
2155
- <ions>5/8</ions>
2156
- <count>1</count>
2157
- <tic>0</tic>
2158
- </peptide>
2159
- </protein>
2160
- <protein>
2161
- <reference>gi|20539418|ref|XP_168226.1| hypothetical protein XP_168226 [Homo sapiens]</reference>
2162
- <protein_probability>2.34E-4</protein_probability>
2163
- <consensus_score>12.0</consensus_score>
2164
- <Sf>0.00</Sf>
2165
- <unified_score>0</unified_score>
2166
- <coverage>0.0</coverage>
2167
- <pI>0.0</pI>
2168
- <weight>12547.9</weight>
2169
- <accession>20539418</accession>
2170
- <peptide>
2171
- <file>7MIX_STD_110802_1, 3603</file>
2172
- <sequence>K.YSCVDLTSNWRK.C</sequence>
2173
- <mass>1472.65</mass>
2174
- <deltamass>0.84</deltamass>
2175
- <charge>2</charge>
2176
- <peptide_probability>2.34E-4</peptide_probability>
2177
- <xcorr>0.986</xcorr>
2178
- <deltacn>0.161</deltacn>
2179
- <sp>220.7</sp>
2180
- <rsp>1</rsp>
2181
- <ions>8/22</ions>
2182
- <count>0</count>
2183
- <tic>10421</tic>
2184
- </peptide>
2185
- <peptide>
2186
- <file>7MIX_STD_110802_1, 5145</file>
2187
- <sequence>K.YNFLLFPLMPLVLFSILRK.H</sequence>
2188
- <mass>2325.93</mass>
2189
- <deltamass>0.10</deltamass>
2190
- <charge>3</charge>
2191
- <peptide_probability>2.34E-4</peptide_probability>
2192
- <xcorr>0.977</xcorr>
2193
- <deltacn>0.078</deltacn>
2194
- <sp>229.9</sp>
2195
- <rsp>1</rsp>
2196
- <ions>14/72</ions>
2197
- <count>0</count>
2198
- <tic>7647</tic>
2199
- </peptide>
2200
- </protein>
2201
- <protein>
2202
- <reference>SHUFF_gi|1787879|gb|AAC74667.1| putative transcriptional regulator LYSR-type [Escherichia coli K12]</reference>
2203
- <protein_probability>2.39E-4</protein_probability>
2204
- <consensus_score>8.1</consensus_score>
2205
- <Sf>0.00</Sf>
2206
- <unified_score>0</unified_score>
2207
- <coverage>0.0</coverage>
2208
- <pI>0.0</pI>
2209
- <weight>33281.1</weight>
2210
- <accession>0</accession>
2211
- <peptide>
2212
- <file>7MIX_STD_110802_1, 3080</file>
2213
- <sequence>K.ALVETDAGDARLLRILHVR.M</sequence>
2214
- <mass>2119.46</mass>
2215
- <deltamass>0.04</deltamass>
2216
- <charge>3</charge>
2217
- <peptide_probability>2.39E-4</peptide_probability>
2218
- <xcorr>1.528</xcorr>
2219
- <deltacn>0.526</deltacn>
2220
- <sp>347.1</sp>
2221
- <rsp>11</rsp>
2222
- <ions>19/72</ions>
2223
- <count>0</count>
2224
- <tic>7239</tic>
2225
- </peptide>
2226
- <peptide>
2227
- <file>7MIX_STD_110802_1, 4982</file>
2228
- <sequence>R.ESAEAFAMQSAMRAEDESLLLAIMPLEFNHK.L</sequence>
2229
- <mass>3481.97</mass>
2230
- <deltamass>1.24</deltamass>
2231
- <charge>3</charge>
2232
- <peptide_probability>2.39E-4</peptide_probability>
2233
- <xcorr>0.973</xcorr>
2234
- <deltacn>0.107</deltacn>
2235
- <sp>119.8</sp>
2236
- <rsp>55</rsp>
2237
- <ions>14/120</ions>
2238
- <count>0</count>
2239
- <tic>8384</tic>
2240
- </peptide>
2241
- </protein>
2242
- <protein>
2243
- <reference>SHUFF_gi|29727445|ref|XP_297286.1| hypothetical protein XP_297286 [Homo sapiens]</reference>
2244
- <protein_probability>2.46E-4</protein_probability>
2245
- <consensus_score>16.1</consensus_score>
2246
- <Sf>0.00</Sf>
2247
- <unified_score>0</unified_score>
2248
- <coverage>0.0</coverage>
2249
- <pI>0.0</pI>
2250
- <weight>19011.5</weight>
2251
- <accession>0</accession>
2252
- <peptide>
2253
- <file>7MIX_STD_110802_1, 2309</file>
2254
- <sequence>K.GLEPNMVTSHRGR.Q</sequence>
2255
- <mass>1454.64</mass>
2256
- <deltamass>0.56</deltamass>
2257
- <charge>2</charge>
2258
- <peptide_probability>2.46E-4</peptide_probability>
2259
- <xcorr>1.342</xcorr>
2260
- <deltacn>0.140</deltacn>
2261
- <sp>257.5</sp>
2262
- <rsp>8</rsp>
2263
- <ions>8/24</ions>
2264
- <count>0</count>
2265
- <tic>11217</tic>
2266
- </peptide>
2267
- <peptide>
2268
- <file>7MIX_STD_110802_1, 6165</file>
2269
- <sequence>R.QEMEGAVEYLKHLEPIR.R</sequence>
2270
- <mass>2043.33</mass>
2271
- <deltamass>0.79</deltamass>
2272
- <charge>2</charge>
2273
- <peptide_probability>2.46E-4</peptide_probability>
2274
- <xcorr>0.858</xcorr>
2275
- <deltacn>0.256</deltacn>
2276
- <sp>134.4</sp>
2277
- <rsp>16</rsp>
2278
- <ions>8/32</ions>
2279
- <count>0</count>
2280
- <tic>9907</tic>
2281
- </peptide>
2282
- </protein>
2283
- <protein>
2284
- <reference>SHUFF_gi|27482335|ref|XP_089558.2| similar to CG15021-PA [Homo sapiens]</reference>
2285
- <protein_probability>2.51E-4</protein_probability>
2286
- <consensus_score>8.0</consensus_score>
2287
- <Sf>0.00</Sf>
2288
- <unified_score>0</unified_score>
2289
- <coverage>0.0</coverage>
2290
- <pI>0.0</pI>
2291
- <weight>18865.2</weight>
2292
- <accession>0</accession>
2293
- <peptide>
2294
- <file>7MIX_STD_110802_1, 3182</file>
2295
- <sequence>-.WEAQSLVLKPTDDLTTPEGFR.G</sequence>
2296
- <mass>2404.66</mass>
2297
- <deltamass>0.21</deltamass>
2298
- <charge>2</charge>
2299
- <peptide_probability>2.51E-4</peptide_probability>
2300
- <xcorr>0.877</xcorr>
2301
- <deltacn>0.210</deltacn>
2302
- <sp>131.4</sp>
2303
- <rsp>10</rsp>
2304
- <ions>8/40</ions>
2305
- <count>0</count>
2306
- <tic>11625</tic>
2307
- </peptide>
2308
- </protein>
2309
- <protein>
2310
- <reference>SHUFF_gi|22062858|ref|XP_059832.2| hypothetical protein XP_059832 [Homo sapiens]</reference>
2311
- <protein_probability>2.74E-4</protein_probability>
2312
- <consensus_score>10.1</consensus_score>
2313
- <Sf>0.00</Sf>
2314
- <unified_score>0</unified_score>
2315
- <coverage>0.0</coverage>
2316
- <pI>0.0</pI>
2317
- <weight>32846.1</weight>
2318
- <accession>0</accession>
2319
- <peptide>
2320
- <file>7MIX_STD_110802_1, 3513</file>
2321
- <sequence>R.YPDKESPSADTK.S</sequence>
2322
- <mass>1338.40</mass>
2323
- <deltamass>1.03</deltamass>
2324
- <charge>2</charge>
2325
- <peptide_probability>2.74E-4</peptide_probability>
2326
- <xcorr>1.808</xcorr>
2327
- <deltacn>0.029</deltacn>
2328
- <sp>147.9</sp>
2329
- <rsp>54</rsp>
2330
- <ions>10/22</ions>
2331
- <count>0</count>
2332
- <tic>3385</tic>
2333
- </peptide>
2334
- </protein>
2335
- <protein>
2336
- <reference>SHUFF_gi|19923911|ref|NP_612395.1| hypothetical protein BC008207 [Homo sapiens]</reference>
2337
- <protein_probability>2.76E-4</protein_probability>
2338
- <consensus_score>14.1</consensus_score>
2339
- <Sf>0.00</Sf>
2340
- <unified_score>0</unified_score>
2341
- <coverage>0.0</coverage>
2342
- <pI>0.0</pI>
2343
- <weight>53702.2</weight>
2344
- <accession>0</accession>
2345
- <peptide>
2346
- <file>7MIX_STD_110802_1, 2034</file>
2347
- <sequence>R.SVDPGPRLPPPTGPLSAHMTQGSIPNIANSVKR.L</sequence>
2348
- <mass>3393.87</mass>
2349
- <deltamass>0.11</deltamass>
2350
- <charge>3</charge>
2351
- <peptide_probability>2.76E-4</peptide_probability>
2352
- <xcorr>1.731</xcorr>
2353
- <deltacn>0.032</deltacn>
2354
- <sp>157.6</sp>
2355
- <rsp>57</rsp>
2356
- <ions>17/128</ions>
2357
- <count>0</count>
2358
- <tic>10450</tic>
2359
- </peptide>
2360
- <peptide>
2361
- <file>7MIX_STD_110802_1, 1797</file>
2362
- <sequence>K.MSYSPAPDIDK.S</sequence>
2363
- <mass>1224.37</mass>
2364
- <deltamass>0.47</deltamass>
2365
- <charge>2</charge>
2366
- <peptide_probability>2.76E-4</peptide_probability>
2367
- <xcorr>1.036</xcorr>
2368
- <deltacn>0.073</deltacn>
2369
- <sp>306.7</sp>
2370
- <rsp>2</rsp>
2371
- <ions>10/20</ions>
2372
- <count>0</count>
2373
- <tic>9741</tic>
2374
- </peptide>
2375
- </protein>
2376
- <protein>
2377
- <reference>SHUFF_gi|4757866|ref|NP_004625.1| bromodomain-containing protein; bromodomain-containing protein, 1</reference>
2378
- <protein_probability>3.01E-4</protein_probability>
2379
- <consensus_score>36.1</consensus_score>
2380
- <Sf>0.00</Sf>
2381
- <unified_score>0</unified_score>
2382
- <coverage>0.0</coverage>
2383
- <pI>0.0</pI>
2384
- <weight>137541.9</weight>
2385
- <accession>0</accession>
2386
- <peptide>
2387
- <file>7MIX_STD_110802_1, 2778</file>
2388
- <sequence>K.AESSEVETESKSLK.D</sequence>
2389
- <mass>1524.61</mass>
2390
- <deltamass>1.31</deltamass>
2391
- <charge>2</charge>
2392
- <peptide_probability>3.01E-4</peptide_probability>
2393
- <xcorr>1.318</xcorr>
2394
- <deltacn>0.014</deltacn>
2395
- <sp>98.2</sp>
2396
- <rsp>165</rsp>
2397
- <ions>7/26</ions>
2398
- <count>0</count>
2399
- <tic>9078</tic>
2400
- </peptide>
2401
- <peptide>
2402
- <file>7MIX_STD_110802_1, 6246</file>
2403
- <sequence>K.DKWDDYPGAYK.C</sequence>
2404
- <mass>1358.44</mass>
2405
- <deltamass>1.28</deltamass>
2406
- <charge>2</charge>
2407
- <peptide_probability>3.01E-4</peptide_probability>
2408
- <xcorr>1.205</xcorr>
2409
- <deltacn>0.146</deltacn>
2410
- <sp>79.3</sp>
2411
- <rsp>33</rsp>
2412
- <ions>7/20</ions>
2413
- <count>0</count>
2414
- <tic>4180</tic>
2415
- </peptide>
2416
- <peptide>
2417
- <file>7MIX_STD_110802_1, 3683</file>
2418
- <sequence>R.CHCR.M</sequence>
2419
- <mass>518.64</mass>
2420
- <deltamass>0.36</deltamass>
2421
- <charge>1</charge>
2422
- <peptide_probability>3.01E-4</peptide_probability>
2423
- <xcorr>0.506</xcorr>
2424
- <deltacn>0.101</deltacn>
2425
- <sp>76.9</sp>
2426
- <rsp>1</rsp>
2427
- <ions>4/6</ions>
2428
- <count>5</count>
2429
- <tic>0</tic>
2430
- </peptide>
2431
- <peptide>
2432
- <file>7MIX_STD_110802_1, 2403</file>
2433
- <sequence>K.CVMKIGVGAEENNR.L</sequence>
2434
- <mass>1520.76</mass>
2435
- <deltamass>0.09</deltamass>
2436
- <charge>2</charge>
2437
- <peptide_probability>3.01E-4</peptide_probability>
2438
- <xcorr>0.971</xcorr>
2439
- <deltacn>0.180</deltacn>
2440
- <sp>154.4</sp>
2441
- <rsp>40</rsp>
2442
- <ions>8/26</ions>
2443
- <count>0</count>
2444
- <tic>9751</tic>
2445
- </peptide>
2446
- <peptide>
2447
- <file>7MIX_STD_110802_1, 4782</file>
2448
- <sequence>K.ESSVGRELKQLDHAK.R</sequence>
2449
- <mass>1697.87</mass>
2450
- <deltamass>1.35</deltamass>
2451
- <charge>2</charge>
2452
- <peptide_probability>3.01E-4</peptide_probability>
2453
- <xcorr>0.497</xcorr>
2454
- <deltacn>1.100</deltacn>
2455
- <sp>33.0</sp>
2456
- <rsp>178</rsp>
2457
- <ions>4/28</ions>
2458
- <count>0</count>
2459
- <tic>5322</tic>
2460
- </peptide>
2461
- </protein>
2462
- <protein>
2463
- <reference>SHUFF_gi|4758030|ref|NP_004362.1| coatomer protein complex, subunit alpha; alpha coat protein; xeni</reference>
2464
- <protein_probability>3.42E-4</protein_probability>
2465
- <consensus_score>12.1</consensus_score>
2466
- <Sf>0.00</Sf>
2467
- <unified_score>0</unified_score>
2468
- <coverage>0.0</coverage>
2469
- <pI>0.0</pI>
2470
- <weight>138330.6</weight>
2471
- <accession>0</accession>
2472
- <peptide>
2473
- <file>7MIX_STD_110802_1, 831 - 833</file>
2474
- <sequence>R.IGLCQSFPAAPSNTGERR.L</sequence>
2475
- <mass>1905.13</mass>
2476
- <deltamass>0.29</deltamass>
2477
- <charge>3</charge>
2478
- <peptide_probability>3.42E-4</peptide_probability>
2479
- <xcorr>2.930</xcorr>
2480
- <deltacn>0.276</deltacn>
2481
- <sp>683.5</sp>
2482
- <rsp>2</rsp>
2483
- <ions>23/68</ions>
2484
- <count>0</count>
2485
- <tic>5876</tic>
2486
- </peptide>
2487
- <peptide>
2488
- <file>7MIX_STD_110802_1, 5927</file>
2489
- <sequence>K.VDHCFR.K</sequence>
2490
- <mass>776.89</mass>
2491
- <deltamass>0.59</deltamass>
2492
- <charge>1</charge>
2493
- <peptide_probability>3.42E-4</peptide_probability>
2494
- <xcorr>0.581</xcorr>
2495
- <deltacn>1.100</deltacn>
2496
- <sp>182.0</sp>
2497
- <rsp>7</rsp>
2498
- <ions>6/10</ions>
2499
- <count>0</count>
2500
- <tic>4185</tic>
2501
- </peptide>
2502
- </protein>
2503
- </sequestresults>