mspire 0.2.4 → 0.3.0

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Files changed (233) hide show
  1. data/INSTALL +1 -0
  2. data/README +25 -0
  3. data/Rakefile +129 -40
  4. data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
  5. data/bin/bioworks_to_pepxml.rb +1 -0
  6. data/bin/fasta_shaker.rb +1 -96
  7. data/bin/filter_and_validate.rb +5 -0
  8. data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
  9. data/bin/prob_validate.rb +6 -0
  10. data/bin/raw_to_mzXML.rb +2 -2
  11. data/bin/srf_group.rb +1 -0
  12. data/bin/srf_to_sqt.rb +40 -0
  13. data/changelog.txt +68 -0
  14. data/lib/align/chams.rb +6 -6
  15. data/lib/align.rb +4 -3
  16. data/lib/bsearch.rb +120 -0
  17. data/lib/fasta.rb +318 -86
  18. data/lib/group_by.rb +10 -0
  19. data/lib/index_by.rb +11 -0
  20. data/lib/merge_deep.rb +21 -0
  21. data/lib/{spec → ms/converter}/mzxml.rb +77 -109
  22. data/lib/ms/gradient_program.rb +171 -0
  23. data/lib/ms/msrun.rb +209 -0
  24. data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
  25. data/lib/ms/parser/mzdata/axml.rb +12 -0
  26. data/lib/ms/parser/mzdata/dom.rb +160 -0
  27. data/lib/ms/parser/mzdata/libxml.rb +7 -0
  28. data/lib/ms/parser/mzdata.rb +25 -0
  29. data/lib/ms/parser/mzxml/axml.rb +11 -0
  30. data/lib/ms/parser/mzxml/dom.rb +159 -0
  31. data/lib/ms/parser/mzxml/hpricot.rb +253 -0
  32. data/lib/ms/parser/mzxml/libxml.rb +15 -0
  33. data/lib/ms/parser/mzxml/regexp.rb +122 -0
  34. data/lib/ms/parser/mzxml/rexml.rb +72 -0
  35. data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
  36. data/lib/ms/parser/mzxml.rb +175 -0
  37. data/lib/ms/parser.rb +108 -0
  38. data/lib/ms/precursor.rb +10 -0
  39. data/lib/ms/scan.rb +81 -0
  40. data/lib/ms/spectrum.rb +193 -0
  41. data/lib/ms.rb +10 -0
  42. data/lib/mspire.rb +4 -0
  43. data/lib/roc.rb +61 -1
  44. data/lib/sample_enzyme.rb +31 -8
  45. data/lib/scan_i.rb +21 -0
  46. data/lib/spec_id/aa_freqs.rb +7 -3
  47. data/lib/spec_id/bioworks.rb +20 -14
  48. data/lib/spec_id/digestor.rb +139 -0
  49. data/lib/spec_id/mass.rb +116 -0
  50. data/lib/spec_id/parser/proph.rb +236 -0
  51. data/lib/spec_id/precision/filter/cmdline.rb +209 -0
  52. data/lib/spec_id/precision/filter/interactive.rb +134 -0
  53. data/lib/spec_id/precision/filter/output.rb +147 -0
  54. data/lib/spec_id/precision/filter.rb +623 -0
  55. data/lib/spec_id/precision/output.rb +60 -0
  56. data/lib/spec_id/precision/prob/cmdline.rb +139 -0
  57. data/lib/spec_id/precision/prob/output.rb +88 -0
  58. data/lib/spec_id/precision/prob.rb +171 -0
  59. data/lib/spec_id/proph/pep_summary.rb +92 -0
  60. data/lib/spec_id/proph/prot_summary.rb +484 -0
  61. data/lib/spec_id/proph.rb +2 -466
  62. data/lib/spec_id/protein_summary.rb +2 -2
  63. data/lib/spec_id/sequest/params.rb +316 -0
  64. data/lib/spec_id/sequest/pepxml.rb +1513 -0
  65. data/lib/spec_id/sequest.rb +2 -1672
  66. data/lib/spec_id/srf.rb +445 -177
  67. data/lib/spec_id.rb +183 -95
  68. data/lib/spec_id_xml.rb +8 -10
  69. data/lib/transmem/phobius.rb +147 -0
  70. data/lib/transmem/toppred.rb +368 -0
  71. data/lib/transmem.rb +157 -0
  72. data/lib/validator/aa.rb +135 -0
  73. data/lib/validator/background.rb +73 -0
  74. data/lib/validator/bias.rb +95 -0
  75. data/lib/validator/cmdline.rb +260 -0
  76. data/lib/validator/decoy.rb +94 -0
  77. data/lib/validator/digestion_based.rb +69 -0
  78. data/lib/validator/probability.rb +48 -0
  79. data/lib/validator/prot_from_pep.rb +234 -0
  80. data/lib/validator/transmem.rb +272 -0
  81. data/lib/validator/true_pos.rb +46 -0
  82. data/lib/validator.rb +214 -0
  83. data/lib/xml.rb +38 -0
  84. data/lib/xml_style_parser.rb +105 -0
  85. data/lib/xmlparser_wrapper.rb +19 -0
  86. data/script/compile_and_plot_smriti_final.rb +97 -0
  87. data/script/extract_gradient_programs.rb +56 -0
  88. data/script/get_apex_values_rexml.rb +44 -0
  89. data/script/mzXML2timeIndex.rb +1 -1
  90. data/script/smriti_final_analysis.rb +103 -0
  91. data/script/toppred_to_yaml.rb +47 -0
  92. data/script/tpp_installer.rb +1 -1
  93. data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
  94. data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
  95. data/specs/bin/fasta_shaker_spec.rb +259 -0
  96. data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
  97. data/specs/bin/filter_and_validate_spec.rb +124 -0
  98. data/specs/bin/ms_to_lmat_spec.rb +34 -0
  99. data/specs/bin/prob_validate_spec.rb +62 -0
  100. data/specs/bin/protein_summary_spec.rb +10 -0
  101. data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
  102. data/specs/gi_spec.rb +22 -0
  103. data/specs/load_bin_path.rb +7 -0
  104. data/specs/merge_deep_spec.rb +13 -0
  105. data/specs/ms/gradient_program_spec.rb +77 -0
  106. data/specs/ms/msrun_spec.rb +455 -0
  107. data/specs/ms/parser_spec.rb +92 -0
  108. data/specs/ms/spectrum_spec.rb +89 -0
  109. data/specs/roc_spec.rb +251 -0
  110. data/specs/rspec_autotest.rb +149 -0
  111. data/specs/sample_enzyme_spec.rb +41 -0
  112. data/specs/spec_helper.rb +133 -0
  113. data/specs/spec_id/aa_freqs_spec.rb +52 -0
  114. data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
  115. data/specs/spec_id/digestor_spec.rb +75 -0
  116. data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
  117. data/specs/spec_id/precision/filter/output_spec.rb +31 -0
  118. data/specs/spec_id/precision/filter_spec.rb +243 -0
  119. data/specs/spec_id/precision/prob_spec.rb +111 -0
  120. data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
  121. data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
  122. data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
  123. data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
  124. data/specs/spec_id/sequest/params_spec.rb +68 -0
  125. data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
  126. data/specs/spec_id/sqt_spec.rb +138 -0
  127. data/specs/spec_id/srf_spec.rb +209 -0
  128. data/specs/spec_id/srf_spec_helper.rb +302 -0
  129. data/specs/spec_id_helper.rb +33 -0
  130. data/specs/spec_id_spec.rb +361 -0
  131. data/specs/spec_id_xml_spec.rb +33 -0
  132. data/specs/transmem/phobius_spec.rb +423 -0
  133. data/specs/transmem/toppred_spec.rb +297 -0
  134. data/specs/transmem_spec.rb +60 -0
  135. data/specs/transmem_spec_shared.rb +64 -0
  136. data/specs/validator/aa_spec.rb +107 -0
  137. data/specs/validator/background_spec.rb +51 -0
  138. data/specs/validator/bias_spec.rb +146 -0
  139. data/specs/validator/decoy_spec.rb +51 -0
  140. data/specs/validator/fasta_helper.rb +26 -0
  141. data/specs/validator/prot_from_pep_spec.rb +141 -0
  142. data/specs/validator/transmem_spec.rb +145 -0
  143. data/specs/validator/true_pos_spec.rb +58 -0
  144. data/specs/validator_helper.rb +33 -0
  145. data/specs/xml_spec.rb +12 -0
  146. data/test_files/000_pepxml18_small.xml +206 -0
  147. data/test_files/020a.mzXML.timeIndex +4710 -0
  148. data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
  149. data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
  150. data/test_files/4-03-03_small-prot.xml +321 -0
  151. data/test_files/4-03-03_small.xml +3876 -0
  152. data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
  153. data/test_files/bioworks-3.3_10prots.xml +5999 -0
  154. data/test_files/bioworks31.params +77 -0
  155. data/test_files/bioworks32.params +62 -0
  156. data/test_files/bioworks33.params +63 -0
  157. data/test_files/bioworks_single_run_small.xml +7237 -0
  158. data/test_files/bioworks_small.fasta +212 -0
  159. data/test_files/bioworks_small.params +63 -0
  160. data/test_files/bioworks_small.phobius +109 -0
  161. data/test_files/bioworks_small.toppred.out +2847 -0
  162. data/test_files/bioworks_small.xml +5610 -0
  163. data/test_files/bioworks_with_INV_small.xml +3753 -0
  164. data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
  165. data/test_files/corrupted_900.srf +0 -0
  166. data/test_files/head_of_7MIX.srf +0 -0
  167. data/test_files/interact-opd1_mods_small-prot.xml +304 -0
  168. data/test_files/messups.fasta +297 -0
  169. data/test_files/opd1/000.my_answer.100lines.xml +101 -0
  170. data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
  171. data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
  172. data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
  173. data/test_files/opd1/000_020-prot.png +0 -0
  174. data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
  175. data/test_files/opd1/000_020_3prots-prot.xml +62 -0
  176. data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
  177. data/test_files/opd1/sequest.3.1.params +77 -0
  178. data/test_files/opd1/sequest.3.2.params +62 -0
  179. data/test_files/opd1/twenty_scans.mzXML +418 -0
  180. data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
  181. data/test_files/opd1/twenty_scans_answ.lmat +0 -0
  182. data/test_files/opd1/twenty_scans_answ.lmata +9 -0
  183. data/test_files/opd1_020_beginning.RAW +0 -0
  184. data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
  185. data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
  186. data/test_files/pepproph_small.xml +4691 -0
  187. data/test_files/phobius.small.noheader.txt +50 -0
  188. data/test_files/phobius.small.small.txt +53 -0
  189. data/test_files/s01_anC1_ld020mM.key.txt +25 -0
  190. data/test_files/s01_anC1_ld020mM.meth +0 -0
  191. data/test_files/small.fasta +297 -0
  192. data/test_files/smallraw.RAW +0 -0
  193. data/test_files/tf_bioworks2excel.bioXML +14340 -0
  194. data/test_files/tf_bioworks2excel.txt.actual +1035 -0
  195. data/test_files/toppred.small.out +416 -0
  196. data/test_files/toppred.xml.out +318 -0
  197. data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
  198. data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
  199. data/test_files/yeast_gly_small-prot.xml +265 -0
  200. data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
  201. data/test_files/yeast_gly_small.xml +3807 -0
  202. data/test_files/yeast_gly_small2.parentTimes +6 -0
  203. metadata +273 -57
  204. data/bin/filter.rb +0 -6
  205. data/bin/precision.rb +0 -5
  206. data/lib/spec/mzdata/parser.rb +0 -108
  207. data/lib/spec/mzdata.rb +0 -48
  208. data/lib/spec/mzxml/parser.rb +0 -449
  209. data/lib/spec/scan.rb +0 -55
  210. data/lib/spec_id/filter.rb +0 -797
  211. data/lib/spec_id/precision.rb +0 -421
  212. data/lib/toppred.rb +0 -18
  213. data/script/filter-peps.rb +0 -164
  214. data/test/tc_aa_freqs.rb +0 -59
  215. data/test/tc_fasta_shaker.rb +0 -149
  216. data/test/tc_filter.rb +0 -203
  217. data/test/tc_filter_peps.rb +0 -46
  218. data/test/tc_gi.rb +0 -17
  219. data/test/tc_id_class_anal.rb +0 -70
  220. data/test/tc_id_precision.rb +0 -89
  221. data/test/tc_msrun.rb +0 -88
  222. data/test/tc_mzxml.rb +0 -88
  223. data/test/tc_mzxml_to_lmat.rb +0 -36
  224. data/test/tc_peptide_parent_times.rb +0 -27
  225. data/test/tc_precision.rb +0 -60
  226. data/test/tc_roc.rb +0 -166
  227. data/test/tc_sample_enzyme.rb +0 -32
  228. data/test/tc_scan.rb +0 -26
  229. data/test/tc_sequest.rb +0 -336
  230. data/test/tc_spec.rb +0 -78
  231. data/test/tc_spec_id.rb +0 -201
  232. data/test/tc_spec_id_xml.rb +0 -36
  233. data/test/tc_srf.rb +0 -262
data/test_files/bioworks_with_SHUFF_small.xml ADDED
@@ -0,0 +1,2503 @@
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+ <?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>
19
+ <charge>2</charge>
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+ <peptide_probability>2.03E-8</peptide_probability>
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+ <xcorr>1.351</xcorr>
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+ <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>
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+ <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>
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+ <xcorr>1.492</xcorr>
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+ <deltacn>0.152</deltacn>
38
+ <sp>316.1</sp>
39
+ <rsp>1</rsp>
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+ <ions>8/12</ions>
41
+ <count>1</count>
42
+ <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>
54
+ <rsp>1</rsp>
55
+ <ions>13/16</ions>
56
+ <count>1</count>
57
+ <tic>0</tic>
58
+ </peptide>
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+ <peptide>
60
+ <file>7MIX_STD_110802_1, 471</file>
61
+ <sequence>R.WVGYGQDSR.L</sequence>
62
+ <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>
72
+ <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>
89
+ <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>
102
+ <tic>0</tic>
103
+ </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>
117
+ <tic>0</tic>
118
+ </peptide>
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+ <peptide>
120
+ <file>7MIX_STD_110802_1, 1443</file>
121
+ <sequence>K.YWQAFR.Q</sequence>
122
+ <mass>870.98</mass>
123
+ <deltamass>0.26</deltamass>
124
+ <charge>2</charge>
125
+ <peptide_probability>2.03E-8</peptide_probability>
126
+ <xcorr>1.699</xcorr>
127
+ <deltacn>0.086</deltacn>
128
+ <sp>357.0</sp>
129
+ <rsp>1</rsp>
130
+ <ions>8/10</ions>
131
+ <count>1</count>
132
+ <tic>0</tic>
133
+ </peptide>
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+ <peptide>
135
+ <file>7MIX_STD_110802_1, 1565</file>
136
+ <sequence>R.IDPNAWVER.W</sequence>
137
+ <mass>1100.21</mass>
138
+ <deltamass>0.24</deltamass>
139
+ <charge>2</charge>
140
+ <peptide_probability>2.03E-8</peptide_probability>
141
+ <xcorr>2.020</xcorr>
142
+ <deltacn>0.339</deltacn>
143
+ <sp>303.6</sp>
144
+ <rsp>1</rsp>
145
+ <ions>13/16</ions>
146
+ <count>1</count>
147
+ <tic>0</tic>
148
+ </peptide>
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+ <peptide>
150
+ <file>7MIX_STD_110802_1, 1569</file>
151
+ <sequence>R.IDPNAWVER.W</sequence>
152
+ <mass>1100.21</mass>
153
+ <deltamass>0.46</deltamass>
154
+ <charge>2</charge>
155
+ <peptide_probability>2.03E-8</peptide_probability>
156
+ <xcorr>2.284</xcorr>
157
+ <deltacn>0.386</deltacn>
158
+ <sp>505.7</sp>
159
+ <rsp>1</rsp>
160
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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>