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/opd1/000.tpp_2.9.2.first10.xml DELETED
@@ -1,126 +0,0 @@
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- <?xml version="1.0" encoding="UTF-8"?>
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- <?xml-stylesheet type="text/xsl" href="/tools/bin/TPP/tpp/schema/pepXML_std.xsl"?>
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- <msms_pipeline_analysis date="2006-08-15T16:36:44" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v18.xsd" summary_xml="000.xml">
4
- <msms_run_summary base_name="/work/john/TPP_pepxml_prep_opd00001/run_000_020_ready/000" msManufacturer="ThermoFinnigan" msModel="LCQ Classic" msIonization="ESI" msMassAnalyzer="Ion Trap" msDetector="UNKNOWN" raw_data_type="raw" raw_data=".mzXML">
5
- <sample_enzyme name="trypsin">
6
- <specificity cut="KR" no_cut="P" sense="C"/>
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- </sample_enzyme>
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- <search_summary base_name="/work/john/TPP_pepxml_prep_opd00001/run_000_020_ready/000" search_engine="SEQUEST" precursor_mass_type="average" fragment_mass_type="average" out_data_type="out" out_data=".tgz" search_id="1">
9
- <search_database local_path="C:\Xcalibur\database\ecoli_K12.fasta" type="AA"/>
10
- <enzymatic_search_constraint enzyme="Trypsin" max_num_internal_cleavages="2" min_number_termini="2"/>
11
- <parameter name="peptide_mass_tol" value="1.500"/>
12
- <parameter name="fragment_ion_tol" value="0.000"/>
13
- <parameter name="ion_series" value=" 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0"/>
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- <parameter name="max_num_differential_AA_per_mod" value="4"/>
15
- <parameter name="nucleotide_reading_frame" value="0"/>
16
- <parameter name="num_output_lines" value="10"/>
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- <parameter name="remove_precursor_peak" value="0"/>
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- <parameter name="ion_cutoff_percentage" value="0.0"/>
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- <parameter name="match_peak_count" value="0"/>
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- <parameter name="match_peak_allowed_error" value="1"/>
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- <parameter name="match_peak_tolerance" value="1.0"/>
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- <parameter name="protein_mass_filter" value="0 0"/>
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- <parameter name="sequence_header_filter" value=""/>
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- </search_summary>
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- <spectrum_query spectrum="000.100.100.1" start_scan="100" end_scan="100" precursor_neutral_mass="1074.5920" assumed_charge="1" index="1">
26
- <search_result> <search_hit hit_rank="1" peptide="SIYFRNFK" peptide_prev_aa="R" peptide_next_aa="G" protein="gi|16130084|ref|NP_416651.1|" num_tot_proteins="1" num_matched_ions=" 4" tot_num_ions=" 14" calc_neutral_pep_mass="1074.1920" massdiff="+0.400000" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
27
- <search_score name="xcorr" value="0.400"/>
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- <search_score name="deltacn" value="0.023"/>
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- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="78.8"/>
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- <search_score name="sprank" value="1"/>
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- </search_hit>
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- </search_result>
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- </spectrum_query>
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- <spectrum_query spectrum="000.1000.1000.1" start_scan="1000" end_scan="1000" precursor_neutral_mass="663.1920" assumed_charge="1" index="2">
36
- <search_result> <search_hit hit_rank="1" peptide="ALADFK" peptide_prev_aa="R" peptide_next_aa="S" protein="gi|16128765|ref|NP_415318.1|" num_tot_proteins="1" num_matched_ions=" 5" tot_num_ions=" 10" calc_neutral_pep_mass="663.7920" massdiff="-0.600000" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
37
- <search_score name="xcorr" value="0.965"/>
38
- <search_score name="deltacn" value="0.132"/>
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- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="81.1"/>
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- <search_score name="sprank" value="1"/>
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- </search_hit>
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- </search_result>
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- </spectrum_query>
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- <spectrum_query spectrum="000.1002.1002.1" start_scan="1002" end_scan="1002" precursor_neutral_mass="1291.6920" assumed_charge="1" index="3">
46
- <search_result> <search_hit hit_rank="1" peptide="EETEWRVQSK" peptide_prev_aa="R" peptide_next_aa="R" protein="gi|16128280|ref|NP_414829.1|" num_tot_proteins="1" num_matched_ions=" 10" tot_num_ions=" 18" calc_neutral_pep_mass="1291.3920" massdiff="+0.300000" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
47
- <search_score name="xcorr" value="0.903"/>
48
- <search_score name="deltacn" value="0.041"/>
49
- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="140.0"/>
51
- <search_score name="sprank" value="1"/>
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- </search_hit>
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- </search_result>
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- </spectrum_query>
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- <spectrum_query spectrum="000.1003.1003.1" start_scan="1003" end_scan="1003" precursor_neutral_mass="769.3920" assumed_charge="1" index="4">
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- <search_result> <search_hit hit_rank="1" peptide="NIGLLNK" peptide_prev_aa="R" peptide_next_aa="I" protein="gi|16129238|ref|NP_415793.1|" num_tot_proteins="1" num_matched_ions=" 8" tot_num_ions=" 12" calc_neutral_pep_mass="770.8920" massdiff="-1.500000" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
57
- <search_score name="xcorr" value="0.887"/>
58
- <search_score name="deltacn" value="0.115"/>
59
- <search_score name="deltacnstar" value="0"/>
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- <search_score name="spscore" value="153.1"/>
61
- <search_score name="sprank" value="2"/>
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- </search_hit>
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- </search_result>
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- </spectrum_query>
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- <spectrum_query spectrum="000.1004.1004.2" start_scan="1004" end_scan="1004" precursor_neutral_mass="1252.2920" assumed_charge="2" index="5">
66
- <search_result> <search_hit hit_rank="1" peptide="QLTYTAHGPHK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131568|ref|NP_418155.1|" num_tot_proteins="1" num_matched_ions=" 7" tot_num_ions=" 20" calc_neutral_pep_mass="1252.3920" massdiff="-0.100000" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
67
- <search_score name="xcorr" value="1.066"/>
68
- <search_score name="deltacn" value="0.172"/>
69
- <search_score name="deltacnstar" value="0"/>
70
- <search_score name="spscore" value="125.2"/>
71
- <search_score name="sprank" value="10"/>
72
- </search_hit>
73
- </search_result>
74
- </spectrum_query>
75
- <spectrum_query spectrum="000.1004.1004.3" start_scan="1004" end_scan="1004" precursor_neutral_mass="1878.4920" assumed_charge="3" index="6">
76
- <search_result> <search_hit hit_rank="1" peptide="AGNARVVNSNAMSFLAQK" peptide_prev_aa="K" peptide_next_aa="G" protein="gi|16131337|ref|NP_417922.1|" num_tot_proteins="1" num_matched_ions=" 16" tot_num_ions=" 68" calc_neutral_pep_mass="1878.0920" massdiff="+0.400000" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
77
- <search_score name="xcorr" value="1.370"/>
78
- <search_score name="deltacn" value="0.199"/>
79
- <search_score name="deltacnstar" value="0"/>
80
- <search_score name="spscore" value="245.0"/>
81
- <search_score name="sprank" value="2"/>
82
- </search_hit>
83
- </search_result>
84
- </spectrum_query>
85
- <spectrum_query spectrum="000.1006.1006.2" start_scan="1006" end_scan="1006" precursor_neutral_mass="888.1920" assumed_charge="2" index="7">
86
- <search_result> <search_hit hit_rank="1" peptide="GNSRDIVK" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16131041|ref|NP_417618.1|" num_tot_proteins="1" num_matched_ions=" 9" tot_num_ions=" 14" calc_neutral_pep_mass="887.9920" massdiff="+0.200000" num_tol_term="2" num_missed_cleavages="1" is_rejected="0">
87
- <search_score name="xcorr" value="0.982"/>
88
- <search_score name="deltacn" value="0.006"/>
89
- <search_score name="deltacnstar" value="0"/>
90
- <search_score name="spscore" value="267.3"/>
91
- <search_score name="sprank" value="6"/>
92
- </search_hit>
93
- </search_result>
94
- </spectrum_query>
95
- <spectrum_query spectrum="000.1006.1006.3" start_scan="1006" end_scan="1006" precursor_neutral_mass="1332.2920" assumed_charge="3" index="8">
96
- <search_result> <search_hit hit_rank="1" peptide="MAAGENPAAEMIK" peptide_prev_aa="K" peptide_next_aa="S" protein="gi|16132265|ref|NP_418563.1|" num_tot_proteins="2" num_matched_ions=" 16" tot_num_ions=" 48" calc_neutral_pep_mass="1332.5920" massdiff="-0.300000" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
97
- <search_score name="xcorr" value="1.058"/>
98
- <search_score name="deltacn" value="0.191"/>
99
- <search_score name="deltacnstar" value="0"/>
100
- <search_score name="spscore" value="177.5"/>
101
- <search_score name="sprank" value="8"/>
102
- </search_hit>
103
- </search_result>
104
- </spectrum_query>
105
- <spectrum_query spectrum="000.1007.1007.1" start_scan="1007" end_scan="1007" precursor_neutral_mass="867.2920" assumed_charge="1" index="9">
106
- <search_result> <search_hit hit_rank="1" peptide="GALLHVEK" peptide_prev_aa="K" peptide_next_aa="M" protein="gi|16128020|ref|NP_414567.1|" num_tot_proteins="1" num_matched_ions=" 4" tot_num_ions=" 14" calc_neutral_pep_mass="865.9920" massdiff="+1.300000" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
107
- <search_score name="xcorr" value="0.467"/>
108
- <search_score name="deltacn" value="0.011"/>
109
- <search_score name="deltacnstar" value="0"/>
110
- <search_score name="spscore" value="39.4"/>
111
- <search_score name="sprank" value="30"/>
112
- </search_hit>
113
- </search_result>
114
- </spectrum_query>
115
- <spectrum_query spectrum="000.1008.1008.2" start_scan="1008" end_scan="1008" precursor_neutral_mass="691.0920" assumed_charge="2" index="10">
116
- <search_result> <search_hit hit_rank="1" peptide="RLFTR" peptide_prev_aa="R" peptide_next_aa="A" protein="gi|16130457|ref|NP_417027.1|" num_tot_proteins="1" num_matched_ions=" 5" tot_num_ions=" 8" calc_neutral_pep_mass="691.7920" massdiff="-0.700000" num_tol_term="2" num_missed_cleavages="0" is_rejected="0">
117
- <search_score name="xcorr" value="0.903"/>
118
- <search_score name="deltacn" value="0.333"/>
119
- <search_score name="deltacnstar" value="0"/>
120
- <search_score name="spscore" value="172.8"/>
121
- <search_score name="sprank" value="1"/>
122
- </search_hit>
123
- </search_result>
124
- </spectrum_query>
125
- </msms_run_summary>
126
- </msms_pipeline_analysis>