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_020-prot.png DELETED
Binary file
data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml DELETED
@@ -1,62 +0,0 @@
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- <?xml version="1.0" encoding="UTF-8"?>
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- <?xml-stylesheet type="text/xsl" href="/work/tpp-data/trial-prot.xsl"?>
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- <protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/protXML /tools/bin/TPP/tpp/bin/../schema/protXML_v4.xsd" summary_xml="/work/tpp-data/trial-prot.xml">
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- <protein_summary_header reference_database="/project/marcotte/ms/database/ecoli_K12.fasta" residue_substitution_list="I -> L" source_files="/work/tpp-data/trial.xml" source_files_alt="/work/tpp-data/trial.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="268.5" num_input_1_spectra="34" num_input_2_spectra="454" num_input_3_spectra="672" initial_min_peptide_prob="0.05" total_no_spectrum_ids="348.3" sample_enzyme="trypsin">
5
- <program_details analysis="proteinprophet" time="2006-08-21T22:29:51" version="4.0(TPP v2.9 GALE rev.2, Build 200608211407)">
6
- <proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" initial_peptide_wt_iters="2" nsp_distribution_iters="1" final_peptide_wt_iters="2" run_options="XML_INPUT">
7
- <nsp_information neighboring_bin_smoothing="Y">
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- <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_excl="0.10" pos_freq="0.623" neg_freq="0.623" pos_to_neg_ratio="1.00"/>
9
- <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.198" neg_freq="0.184" pos_to_neg_ratio="1.07"/>
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- <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.075" neg_freq="0.074" pos_to_neg_ratio="1.02" alt_pos_to_neg_ratio="1.07"/>
11
- <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.063" neg_freq="0.074" pos_to_neg_ratio="0.85" alt_pos_to_neg_ratio="1.07"/>
12
- <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.023" neg_freq="0.026" pos_to_neg_ratio="0.87" alt_pos_to_neg_ratio="1.07"/>
13
- <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.007" neg_freq="0.007" pos_to_neg_ratio="0.97" alt_pos_to_neg_ratio="1.07"/>
14
- <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.006" neg_freq="0.006" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.07"/>
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- <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.006" neg_freq="0.006" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.07"/>
16
- </nsp_information> <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.715" predicted_num_correct="268" predicted_num_incorrect="675" />
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- <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.497" predicted_num_correct="268" predicted_num_incorrect="266" />
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- <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.497" predicted_num_correct="268" predicted_num_incorrect="266" />
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- <protein_summary_data_filter min_probability="0.30" sensitivity="0.881" false_positive_error_rate="0.415" predicted_num_correct="237" predicted_num_incorrect="167" />
20
- <protein_summary_data_filter min_probability="0.40" sensitivity="0.759" false_positive_error_rate="0.336" predicted_num_correct="204" predicted_num_incorrect="103" />
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- <protein_summary_data_filter min_probability="0.50" sensitivity="0.654" false_positive_error_rate="0.281" predicted_num_correct="176" predicted_num_incorrect="68" />
22
- <protein_summary_data_filter min_probability="0.60" sensitivity="0.514" false_positive_error_rate="0.211" predicted_num_correct="138" predicted_num_incorrect="37" />
23
- <protein_summary_data_filter min_probability="0.70" sensitivity="0.380" false_positive_error_rate="0.143" predicted_num_correct="102" predicted_num_incorrect="17" />
24
- <protein_summary_data_filter min_probability="0.80" sensitivity="0.220" false_positive_error_rate="0.030" predicted_num_correct="59" predicted_num_incorrect="2" />
25
- <protein_summary_data_filter min_probability="0.90" sensitivity="0.205" false_positive_error_rate="0.016" predicted_num_correct="55" predicted_num_incorrect="1" />
26
- <protein_summary_data_filter min_probability="0.95" sensitivity="0.181" false_positive_error_rate="0.008" predicted_num_correct="49" predicted_num_incorrect="0" />
27
- <protein_summary_data_filter min_probability="0.96" sensitivity="0.178" false_positive_error_rate="0.007" predicted_num_correct="48" predicted_num_incorrect="0" />
28
- <protein_summary_data_filter min_probability="0.97" sensitivity="0.170" false_positive_error_rate="0.006" predicted_num_correct="46" predicted_num_incorrect="0" />
29
- <protein_summary_data_filter min_probability="0.98" sensitivity="0.163" false_positive_error_rate="0.005" predicted_num_correct="44" predicted_num_incorrect="0" />
30
- <protein_summary_data_filter min_probability="0.99" sensitivity="0.149" false_positive_error_rate="0.003" predicted_num_correct="40" predicted_num_incorrect="0" />
31
- <protein_summary_data_filter min_probability="1.00" sensitivity="0.104" false_positive_error_rate="0.000" predicted_num_correct="28" predicted_num_incorrect="0" />
32
- </proteinprophet_details>
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- </program_details>
34
- </protein_summary_header>
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- <dataset_derivation generation_no="0">
36
- </dataset_derivation>
37
- <protein_group group_number="1" probability="1.00">
38
- <protein protein_name="gi|16128297|ref|NP_414846.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="1.4" unique_stripped_peptides="RAVDILR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.56">
39
- <annotation protein_description="NAD+-dependent betaine aldehyde dehydrogenase [Escherichia coli K12]"/>
40
- <peptide peptide_sequence="RAVDILR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="841.9920">
41
- </peptide>
42
- </protein>
43
- </protein_group>
44
- <protein_group group_number="2" probability="1.00">
45
- <protein protein_name="gi|16132019|ref|NP_418618.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="13.0" unique_stripped_peptides="FRDGLK+AIQFAQDVGIRVIQLAGYDVYYQEANNETRR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.41">
46
- <annotation protein_description="putative hexulose-6-phosphate isomerase [Escherichia coli K12]"/>
47
- <peptide peptide_sequence="FRDGLK" charge="1" initial_probability="0.90" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.42" n_sibling_peptides_bin="2" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="734.8920">
48
- </peptide>
49
- <peptide peptide_sequence="AIQFAQDVGIRVIQLAGYDVYYQEANNETRR" charge="3" initial_probability="0.32" nsp_adjusted_probability="0.42" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="3601.9920">
50
- </peptide>
51
- </protein>
52
- </protein_group>
53
- <protein_group group_number="41" probability="0.98">
54
- <protein protein_name="gi|16128237|ref|NP_414786.1|" n_indistinguishable_proteins="2" probability="0.98" percent_coverage="4.4" unique_stripped_peptides="GGLSGRNAKGGR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.46">
55
- <annotation protein_description="orf, hypothetical protein [Escherichia coli K12]"/>
56
- <indistinguishable_protein protein_name="gi|16130551|ref|NP_417122.1|">
57
- <annotation protein_description="orf, hypothetical protein [Escherichia coli K12]"/> </indistinguishable_protein>
58
- <peptide peptide_sequence="GGLSGRNAKGGR" charge="2" initial_probability="0.99" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1129.1920">
59
- </peptide>
60
- </protein>
61
- </protein_group>
62
- </protein_summary>
data/test_files/opd1/000_020_3prots-prot.xml DELETED
@@ -1,62 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <?xml-stylesheet type="text/xsl" href="/work/tpp-data/trial-prot.xsl"?>
3
- <protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/protXML /tools/bin/TPP/tpp/bin/../schema/protXML_v4.xsd" summary_xml="/work/tpp-data/trial-prot.xml">
4
- <protein_summary_header reference_database="/project/marcotte/ms/database/ecoli_K12.fasta" residue_substitution_list="I -> L" source_files="/work/tpp-data/trial.xml" source_files_alt="/work/tpp-data/trial.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="268.5" num_input_1_spectra="34" num_input_2_spectra="454" num_input_3_spectra="672" initial_min_peptide_prob="0.05" total_no_spectrum_ids="348.3" sample_enzyme="trypsin">
5
- <program_details analysis="proteinprophet" time="2006-08-21T22:29:51" version="4.0(TPP v2.9 GALE rev.2, Build 200608211407)">
6
- <proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" initial_peptide_wt_iters="2" nsp_distribution_iters="1" final_peptide_wt_iters="2" run_options="XML_INPUT">
7
- <nsp_information neighboring_bin_smoothing="Y">
8
- <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_excl="0.10" pos_freq="0.623" neg_freq="0.623" pos_to_neg_ratio="1.00"/>
9
- <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.198" neg_freq="0.184" pos_to_neg_ratio="1.07"/>
10
- <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.075" neg_freq="0.074" pos_to_neg_ratio="1.02" alt_pos_to_neg_ratio="1.07"/>
11
- <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.063" neg_freq="0.074" pos_to_neg_ratio="0.85" alt_pos_to_neg_ratio="1.07"/>
12
- <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.023" neg_freq="0.026" pos_to_neg_ratio="0.87" alt_pos_to_neg_ratio="1.07"/>
13
- <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.007" neg_freq="0.007" pos_to_neg_ratio="0.97" alt_pos_to_neg_ratio="1.07"/>
14
- <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.006" neg_freq="0.006" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.07"/>
15
- <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.006" neg_freq="0.006" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.07"/>
16
- </nsp_information> <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.715" predicted_num_correct="268" predicted_num_incorrect="675" />
17
- <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.497" predicted_num_correct="268" predicted_num_incorrect="266" />
18
- <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.497" predicted_num_correct="268" predicted_num_incorrect="266" />
19
- <protein_summary_data_filter min_probability="0.30" sensitivity="0.881" false_positive_error_rate="0.415" predicted_num_correct="237" predicted_num_incorrect="167" />
20
- <protein_summary_data_filter min_probability="0.40" sensitivity="0.759" false_positive_error_rate="0.336" predicted_num_correct="204" predicted_num_incorrect="103" />
21
- <protein_summary_data_filter min_probability="0.50" sensitivity="0.654" false_positive_error_rate="0.281" predicted_num_correct="176" predicted_num_incorrect="68" />
22
- <protein_summary_data_filter min_probability="0.60" sensitivity="0.514" false_positive_error_rate="0.211" predicted_num_correct="138" predicted_num_incorrect="37" />
23
- <protein_summary_data_filter min_probability="0.70" sensitivity="0.380" false_positive_error_rate="0.143" predicted_num_correct="102" predicted_num_incorrect="17" />
24
- <protein_summary_data_filter min_probability="0.80" sensitivity="0.220" false_positive_error_rate="0.030" predicted_num_correct="59" predicted_num_incorrect="2" />
25
- <protein_summary_data_filter min_probability="0.90" sensitivity="0.205" false_positive_error_rate="0.016" predicted_num_correct="55" predicted_num_incorrect="1" />
26
- <protein_summary_data_filter min_probability="0.95" sensitivity="0.181" false_positive_error_rate="0.008" predicted_num_correct="49" predicted_num_incorrect="0" />
27
- <protein_summary_data_filter min_probability="0.96" sensitivity="0.178" false_positive_error_rate="0.007" predicted_num_correct="48" predicted_num_incorrect="0" />
28
- <protein_summary_data_filter min_probability="0.97" sensitivity="0.170" false_positive_error_rate="0.006" predicted_num_correct="46" predicted_num_incorrect="0" />
29
- <protein_summary_data_filter min_probability="0.98" sensitivity="0.163" false_positive_error_rate="0.005" predicted_num_correct="44" predicted_num_incorrect="0" />
30
- <protein_summary_data_filter min_probability="0.99" sensitivity="0.149" false_positive_error_rate="0.003" predicted_num_correct="40" predicted_num_incorrect="0" />
31
- <protein_summary_data_filter min_probability="1.00" sensitivity="0.104" false_positive_error_rate="0.000" predicted_num_correct="28" predicted_num_incorrect="0" />
32
- </proteinprophet_details>
33
- </program_details>
34
- </protein_summary_header>
35
- <dataset_derivation generation_no="0">
36
- </dataset_derivation>
37
- <protein_group group_number="1" probability="1.00">
38
- <protein protein_name="gi|16128297|ref|NP_414846.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="1.4" unique_stripped_peptides="RAVDILR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.56">
39
- <annotation protein_description="NAD+-dependent betaine aldehyde dehydrogenase [Escherichia coli K12]"/>
40
- <peptide peptide_sequence="RAVDILR" charge="2" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="841.9920">
41
- </peptide>
42
- </protein>
43
- </protein_group>
44
- <protein_group group_number="2" probability="1.00">
45
- <protein protein_name="gi|16132019|ref|NP_418618.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="13.0" unique_stripped_peptides="FRDGLK+AIQFAQDVGIRVIQLAGYDVYYQEANNETRR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.41">
46
- <annotation protein_description="putative hexulose-6-phosphate isomerase [Escherichia coli K12]"/>
47
- <peptide peptide_sequence="FRDGLK" charge="1" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.42" n_sibling_peptides_bin="2" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="734.8920">
48
- </peptide>
49
- <peptide peptide_sequence="AIQFAQDVGIRVIQLAGYDVYYQEANNETRR" charge="3" initial_probability="0.42" nsp_adjusted_probability="0.42" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="3601.9920">
50
- </peptide>
51
- </protein>
52
- </protein_group>
53
- <protein_group group_number="41" probability="0.98">
54
- <protein protein_name="gi|16128237|ref|NP_414786.1|" n_indistinguishable_proteins="2" probability="0.98" percent_coverage="4.4" unique_stripped_peptides="GGLSGRNAKGGR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.46">
55
- <annotation protein_description="orf, hypothetical protein [Escherichia coli K12]"/>
56
- <indistinguishable_protein protein_name="gi|16130551|ref|NP_417122.1|">
57
- <annotation protein_description="orf, hypothetical protein [Escherichia coli K12]"/> </indistinguishable_protein>
58
- <peptide peptide_sequence="GGLSGRNAKGGR" charge="2" initial_probability="0.98" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1129.1920">
59
- </peptide>
60
- </protein>
61
- </protein_group>
62
- </protein_summary>
data/test_files/opd1/opd1_cat_inv_small-prot.xml DELETED
@@ -1,139 +0,0 @@
1
- <?xml version="1.0" encoding="UTF-8"?>
2
- <?xml-stylesheet type="text/xsl" href="/work/tpp-data/opd1_cat_inv-prot.xsl"?>
3
- <protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://regis-web.systemsbiology.net/protXML /tools/bin/TPP/tpp/bin/../schema/protXML_v4.xsd" summary_xml="/work/tpp-data/opd1_cat_inv-prot.xml">
4
- <protein_summary_header reference_database="/project/marcotte/ms/database/ecoli_K12_ncbi_20060321_CAT_INV.fasta" residue_substitution_list="I -> L" source_files="/work/tpp-data/opd1_cat_inv.xml" source_files_alt="/work/tpp-data/opd1_cat_inv.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="1329.6" num_input_1_spectra="12" num_input_2_spectra="646" num_input_3_spectra="6239" initial_min_peptide_prob="0.05" total_no_spectrum_ids="2039.5" sample_enzyme="trypsin">
5
- <program_details analysis="proteinprophet" time="2006-08-30T15:35:12" version="4.0(TPP v2.9 GALE rev.2, Build 200608211407)">
6
- <proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" initial_peptide_wt_iters="2" nsp_distribution_iters="1" final_peptide_wt_iters="1" run_options="XML_INPUT">
7
- <nsp_information neighboring_bin_smoothing="Y">
8
- <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_excl="0.10" pos_freq="0.403" neg_freq="0.416" pos_to_neg_ratio="0.97"/>
9
- <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.183" neg_freq="0.185" pos_to_neg_ratio="0.99" alt_pos_to_neg_ratio="0.97"/>
10
- <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.128" neg_freq="0.132" pos_to_neg_ratio="0.97" alt_pos_to_neg_ratio="0.99"/>
11
- <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.148" neg_freq="0.147" pos_to_neg_ratio="1.00"/>
12
- <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.096" neg_freq="0.090" pos_to_neg_ratio="1.06"/>
13
- <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.035" neg_freq="0.026" pos_to_neg_ratio="1.37"/>
14
- <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.006" neg_freq="0.003" pos_to_neg_ratio="1.64"/>
15
- <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.001" neg_freq="0.001" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.64"/>
16
- </nsp_information> <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.660" predicted_num_correct="1330" predicted_num_incorrect="2586" />
17
- <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.428" predicted_num_correct="1330" predicted_num_incorrect="995" />
18
- <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.428" predicted_num_correct="1330" predicted_num_incorrect="995" />
19
- <protein_summary_data_filter min_probability="0.30" sensitivity="0.922" false_positive_error_rate="0.355" predicted_num_correct="1226" predicted_num_incorrect="675" />
20
- <protein_summary_data_filter min_probability="0.40" sensitivity="0.831" false_positive_error_rate="0.287" predicted_num_correct="1105" predicted_num_incorrect="444" />
21
- <protein_summary_data_filter min_probability="0.50" sensitivity="0.744" false_positive_error_rate="0.233" predicted_num_correct="990" predicted_num_incorrect="300" />
22
- <protein_summary_data_filter min_probability="0.60" sensitivity="0.637" false_positive_error_rate="0.176" predicted_num_correct="847" predicted_num_incorrect="180" />
23
- <protein_summary_data_filter min_probability="0.70" sensitivity="0.517" false_positive_error_rate="0.120" predicted_num_correct="688" predicted_num_incorrect="93" />
24
- <protein_summary_data_filter min_probability="0.80" sensitivity="0.386" false_positive_error_rate="0.060" predicted_num_correct="513" predicted_num_incorrect="33" />
25
- <protein_summary_data_filter min_probability="0.90" sensitivity="0.282" false_positive_error_rate="0.017" predicted_num_correct="375" predicted_num_incorrect="6" />
26
- <protein_summary_data_filter min_probability="0.95" sensitivity="0.247" false_positive_error_rate="0.007" predicted_num_correct="329" predicted_num_incorrect="2" />
27
- <protein_summary_data_filter min_probability="0.96" sensitivity="0.239" false_positive_error_rate="0.006" predicted_num_correct="318" predicted_num_incorrect="2" />
28
- <protein_summary_data_filter min_probability="0.97" sensitivity="0.231" false_positive_error_rate="0.005" predicted_num_correct="307" predicted_num_incorrect="1" />
29
- <protein_summary_data_filter min_probability="0.98" sensitivity="0.223" false_positive_error_rate="0.004" predicted_num_correct="296" predicted_num_incorrect="1" />
30
- <protein_summary_data_filter min_probability="0.99" sensitivity="0.209" false_positive_error_rate="0.003" predicted_num_correct="278" predicted_num_incorrect="1" />
31
- <protein_summary_data_filter min_probability="1.00" sensitivity="0.156" false_positive_error_rate="0.000" predicted_num_correct="208" predicted_num_incorrect="0" />
32
- </proteinprophet_details>
33
- </program_details>
34
- </protein_summary_header>
35
- <dataset_derivation generation_no="0">
36
- </dataset_derivation>
37
- <protein_group group_number="1" probability="1.00">
38
- <protein protein_name="INV_gi|16131365|ref|NP_417950.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="10.0" unique_stripped_peptides="QDLSLKDYSEVDTTLMGK+TRTIEYGTANMNVVFGAPAVGILVLMVLGIGK" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.08">
39
- <annotation protein_description="low-affinity phosphate transport [Escherichia coli K12]"/>
40
- <peptide peptide_sequence="TRTIEYGTANMNVVFGAPAVGILVLMVLGIGK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.69" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="3305.96206">
41
- </peptide>
42
- <peptide peptide_sequence="QDLSLKDYSEVDTTLMGK" charge="3" initial_probability="0.69" nsp_adjusted_probability="0.70" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.00" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2043.26206">
43
- </peptide>
44
- </protein>
45
- </protein_group>
46
- <protein_group group_number="2" probability="1.00">
47
- <protein protein_name="INV_gi|16130377|ref|NP_416947.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="7.4" unique_stripped_peptides="TLLLVMPYAGLLVCSISGIVEIARMVEGPK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.05">
48
- <annotation protein_description="ethanolamine utilization; homolog of Salmonella putative transport protein [Escherichia coli K12]"/>
49
- <peptide peptide_sequence="TLLLVMPYAGLLVCSISGIVEIARMVEGPK" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="3173.91206">
50
- </peptide>
51
- </protein>
52
- </protein_group>
53
- <protein_group group_number="3" probability="1.00">
54
- <protein protein_name="gi|16131182|ref|NP_417762.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="37.1" unique_stripped_peptides="VFMQPASEGTGIIAGGAMR+AVLEVAGVHNVLAK+AYGSTNPINVVR+NMINVALNNGTLQHPVK" group_sibling_id="a" total_number_peptides="7" pct_spectrum_ids="0.29">
55
- <annotation protein_description="30S ribosomal protein S5 [Escherichia coli K12]"/>
56
- <peptide peptide_sequence="AVLEVAGVHNVLAK" charge="2" initial_probability="0.97" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.63" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1419.67206">
57
- </peptide>
58
- <peptide peptide_sequence="VFMQPASEGTGIIAGGAMR" charge="2" initial_probability="0.95" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.65" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1893.20206">
59
- </peptide>
60
- <peptide peptide_sequence="AYGSTNPINVVR" charge="2" initial_probability="0.88" nsp_adjusted_probability="0.91" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.72" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1290.43206">
61
- </peptide>
62
- <peptide peptide_sequence="NMINVALNNGTLQHPVK" charge="2" initial_probability="0.80" nsp_adjusted_probability="0.84" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.81" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="Y" calc_neutral_pep_mass="1863.15206">
63
- </peptide>
64
- </protein>
65
- </protein_group>
66
- <protein_group group_number="4" probability="1.00">
67
- <protein protein_name="gi|16131115|ref|NP_417692.1|" n_indistinguishable_proteins="1" probability="1.00" percent_coverage="4.0" unique_stripped_peptides="VIDLLIKTGVFR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.05">
68
- <annotation protein_description="N-acetylneuraminate lyase [Escherichia coli K12]"/>
69
- <peptide peptide_sequence="VIDLLIKTGVFR" charge="3" initial_probability="1.00" nsp_adjusted_probability="1.00" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1373.69206">
70
- </peptide>
71
- </protein>
72
- </protein_group>
73
- <protein_group group_number="281" probability="0.98">
74
- <protein protein_name="gi|90111270|ref|NP_415941.4|" n_indistinguishable_proteins="1" probability="0.98" percent_coverage="6.5" unique_stripped_peptides="AVKAGDEFAFQYR+IQFDWYPTSDSTDPVDMRMYLR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.05">
75
- <annotation protein_description="putative enzyme [Escherichia coli K12]"/>
76
- <peptide peptide_sequence="IQFDWYPTSDSTDPVDMRMYLR" charge="3" initial_probability="0.98" nsp_adjusted_probability="0.98" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2737.04206">
77
- </peptide>
78
- <peptide peptide_sequence="AVKAGDEFAFQYR" charge="3" initial_probability="0.08" nsp_adjusted_probability="0.08" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.98" n_sibling_peptides_bin="3" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1501.65206">
79
- </peptide>
80
- </protein>
81
- </protein_group>
82
- <protein_group group_number="302" probability="0.97">
83
- <protein protein_name="gi|16128870|ref|NP_415423.1|" n_indistinguishable_proteins="1" probability="0.97" percent_coverage="10.5" unique_stripped_peptides="GDVLNYDEVMER+IIGDYRRVALYGIDYLMK+YSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIK+SGVLTGLPDAYGR" group_sibling_id="a" total_number_peptides="3" pct_spectrum_ids="0.10">
84
- <annotation protein_description="formate acetyltransferase 1 [Escherichia coli K12]"/>
85
- <peptide peptide_sequence="GDVLNYDEVMER" charge="2" initial_probability="0.79" nsp_adjusted_probability="0.80" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.17" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1439.55206">
86
- </peptide>
87
- <peptide peptide_sequence="SGVLTGLPDAYGR" charge="2" initial_probability="0.75" nsp_adjusted_probability="0.76" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.21" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1305.44206">
88
- </peptide>
89
- <peptide peptide_sequence="YSYEASLMALHDRDVIRTMACGIAGLSVAADSLSAIK" charge="3" initial_probability="0.42" nsp_adjusted_probability="0.42" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.54" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="3900.48206">
90
- </peptide>
91
- <peptide peptide_sequence="IIGDYRRVALYGIDYLMK" charge="3" initial_probability="0.05" nsp_adjusted_probability="0.05" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.96" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="2159.56206">
92
- </peptide>
93
- </protein>
94
- </protein_group>
95
- <protein_group group_number="303" probability="0.97">
96
- <protein protein_name="gi|90111652|ref|NP_418264.4|" n_indistinguishable_proteins="1" probability="0.97" percent_coverage="9.7" unique_stripped_peptides="HETISEDELRQRLSR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.05">
97
- <annotation protein_description="hypothetical protein b3820 [Escherichia coli K12]"/>
98
- <peptide peptide_sequence="HETISEDELRQRLSR" charge="3" initial_probability="0.97" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1869.01206">
99
- </peptide>
100
- </protein>
101
- </protein_group>
102
- <protein_group group_number="304" probability="0.97">
103
- <protein protein_name="gi|16128170|ref|NP_414719.1|" n_indistinguishable_proteins="1" probability="0.97" percent_coverage="11.6" unique_stripped_peptides="VNLTGKVTIPGSDNEYYK+REMRQMEGAWLGSDLVDQGK+DGDTLLVQVKERPTIASITFSGNK+EMRQMEGAWLGSDLVDQGK+SDDAVGGNAMAVASLEFITPTPFISDK+DAVLRREMR" group_sibling_id="a" total_number_peptides="4" pct_spectrum_ids="0.12">
104
- <annotation protein_description="putative outer membrane antigen [Escherichia coli K12]"/>
105
- <peptide peptide_sequence="DGDTLLVQVKERPTIASITFSGNK" charge="3" initial_probability="0.79" nsp_adjusted_probability="0.80" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.42" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2589.90206">
106
- </peptide>
107
- <peptide peptide_sequence="SDDAVGGNAMAVASLEFITPTPFISDK" charge="3" initial_probability="0.67" nsp_adjusted_probability="0.68" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.54" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2754.04206">
108
- </peptide>
109
- <peptide peptide_sequence="REMRQMEGAWLGSDLVDQGK" charge="3" initial_probability="0.42" nsp_adjusted_probability="0.42" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.79" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2306.59206">
110
- </peptide>
111
- <peptide peptide_sequence="DAVLRREMR" charge="3" initial_probability="0.23" nsp_adjusted_probability="0.23" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.98" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1145.34206">
112
- </peptide>
113
- <peptide peptide_sequence="EMRQMEGAWLGSDLVDQGK" charge="3" initial_probability="0.10" nsp_adjusted_probability="0.10" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.11" n_sibling_peptides_bin="5" n_instances="2" is_contributing_evidence="N" calc_neutral_pep_mass="2150.40206">
114
- </peptide>
115
- <peptide peptide_sequence="VNLTGKVTIPGSDNEYYK" charge="3" initial_probability="0.09" nsp_adjusted_probability="0.09" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.21" n_sibling_peptides_bin="5" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1998.20206">
116
- </peptide>
117
- </protein>
118
- </protein_group>
119
- <protein_group group_number="305" probability="0.97">
120
- <protein protein_name="gi|16128077|ref|NP_414626.1|" n_indistinguishable_proteins="1" probability="0.97" percent_coverage="3.1" unique_stripped_peptides="TVVHMMESVALPGGGGVK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="0.05">
121
- <annotation protein_description="division-specific transpeptidase, penicillin-binding protein 3 [Escherichia coli K12]"/>
122
- <peptide peptide_sequence="TVVHMMESVALPGGGGVK" charge="3" initial_probability="0.97" nsp_adjusted_probability="0.97" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1769.10206">
123
- </peptide>
124
- </protein>
125
- </protein_group>
126
- <protein_group group_number="306" probability="0.97">
127
- <protein protein_name="INV_gi|90111252|ref|NP_415854.4|" n_indistinguishable_proteins="1" probability="0.97" percent_coverage="14.4" unique_stripped_peptides="AMMLTADESGAPAEVR+TGEEAPQFILKIVGHLGSEFQK+ENHHGAALQTGFVVYSAQGQHQQVRAMMLTADESGAPAEVR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="0.07">
128
- <annotation protein_description="aminobenzoyl-glutamate utilization protein [Escherichia coli K12]"/>
129
- <peptide peptide_sequence="AMMLTADESGAPAEVR" charge="3" initial_probability="0.95" nsp_adjusted_probability="0.95" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.41" n_sibling_peptides_bin="2" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="1648.86206">
130
- </peptide>
131
- <peptide peptide_sequence="TGEEAPQFILKIVGHLGSEFQK" charge="3" initial_probability="0.28" nsp_adjusted_probability="0.28" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.08" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="Y" calc_neutral_pep_mass="2428.75206">
132
- </peptide>
133
- <peptide peptide_sequence="AMMLTADESGAPAEVR" charge="2" initial_probability="0.13" nsp_adjusted_probability="0.13" peptide_group_designator="a" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.23" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="1648.86206">
134
- </peptide>
135
- <peptide peptide_sequence="ENHHGAALQTGFVVYSAQGQHQQVRAMMLTADESGAPAEVR" charge="3" initial_probability="0.07" nsp_adjusted_probability="0.07" weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.36" n_sibling_peptides_bin="4" n_instances="1" is_contributing_evidence="N" calc_neutral_pep_mass="4393.81206">
136
- </peptide>
137
- </protein>
138
- </protein_group>
139
- </protein_summary>
data/test_files/opd1/sequest.3.1.params DELETED
@@ -1,77 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\ecoli_K12.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 1.5000
5
- ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
6
- fragment_ion_tolerance = 0.0000 ; leave at 0.0 unless you have real poor data
7
- num_output_lines = 10 ; # peptide results to show
8
- num_results = 500 ; # results to store
9
- num_description_lines = 5 ; # full protein descriptions to show for top N peptides
10
- show_fragment_ions = 1 ; 0=no, 1=yes
11
- print_duplicate_references = 40 ; 0=no, 1=yes
12
- enzyme_number = 1
13
- max_num_differential_AA_per_mod = 4 ; max # of modified AA per diff. mod in a peptide
14
- diff_search_options = 0.0000 S 0.0000 C 0.0000 M 0.0000 X 0.0000 T 0.0000 Y
15
- term_diff_search_options = 0.0000 0.0000
16
- nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
17
- mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
18
- mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
19
- normalize_xcorr = 0 ; use normalized xcorr values in the out file
20
- remove_precursor_peak = 0 ; 0=no, 1=yes
21
- ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
22
- max_num_internal_cleavage_sites = 2 ; maximum value is 5
23
- protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
24
- match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
25
- match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
26
- match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
27
- create_output_files = 1 ; 0=no, 1=yes
28
- partial_sequence =
29
- sequence_header_filter =
30
-
31
- add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
32
- add_Cterm_protein = 0.0000 ; added to each protein C-terminus
33
- add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
34
- add_Nterm_protein = 0.0000 ; added to each protein N-terminus
35
- add_G_Glycine = 0.0000 ; added to G - avg. 57.0519, mono. 57.02146
36
- add_A_Alanine = 0.0000 ; added to A - avg. 71.0788, mono. 71.03711
37
- add_S_Serine = 0.0000 ; added to S - avg. 87.0782, mono. 87.02303
38
- add_P_Proline = 0.0000 ; added to P - avg. 97.1167, mono. 97.05276
39
- add_V_Valine = 0.0000 ; added to V - avg. 99.1326, mono. 99.06841
40
- add_T_Threonine = 0.0000 ; added to T - avg. 101.1051, mono. 101.04768
41
- add_C_Cysteine = 0.0000 ; added to C - avg. 103.1388, mono. 103.00919
42
- add_L_Leucine = 0.0000 ; added to L - avg. 113.1594, mono. 113.08406
43
- add_I_Isoleucine = 0.0000 ; added to I - avg. 113.1594, mono. 113.08406
44
- add_X_LorI = 0.0000 ; added to X - avg. 113.1594, mono. 113.08406
45
- add_N_Asparagine = 0.0000 ; added to N - avg. 114.1038, mono. 114.04293
46
- add_O_Ornithine = 0.0000 ; added to O - avg. 114.1472, mono 114.07931
47
- add_B_avg_NandD = 0.0000 ; added to B - avg. 114.5962, mono. 114.53494
48
- add_D_Aspartic_Acid = 0.0000 ; added to D - avg. 115.0886, mono. 115.02694
49
- add_Q_Glutamine = 0.0000 ; added to Q - avg. 128.1307, mono. 128.05858
50
- add_K_Lysine = 0.0000 ; added to K - avg. 128.1741, mono. 128.09496
51
- add_Z_avg_QandE = 0.0000 ; added to Z - avg. 128.6231, mono. 128.55059
52
- add_E_Glutamic_Acid = 0.0000 ; added to E - avg. 129.1155, mono. 129.04259
53
- add_M_Methionine = 0.0000 ; added to M - avg. 131.1926, mono. 131.04049
54
- add_H_Histidine = 0.0000 ; added to H - avg. 137.1411, mono. 137.05891
55
- add_F_Phenylalanine = 0.0000 ; added to F - avg. 147.1766, mono. 147.06841
56
- add_R_Arginine = 0.0000 ; added to R - avg. 156.1875, mono. 156.10111
57
- add_Y_Tyrosine = 0.0000 ; added to Y - avg. 163.1760, mono. 163.06333
58
- add_W_Tryptophan = 0.0000 ; added to W - avg. 186.2132, mono. 186.07931
59
-
60
- [SEQUEST_ENZYME_INFO]
61
- 0. No_Enzyme 0 - -
62
- 1. Trypsin 1 KR -
63
- 2. Trypsin(KRLNH) 1 KRLNH -
64
- 3. Chymotrypsin 1 FWYL -
65
- 4. Chymotrypsin(FWY) 1 FWY P
66
- 5. Clostripain 1 R -
67
- 6. Cyanogen_Bromide 1 M -
68
- 7. IodosoBenzoate 1 W -
69
- 8. Proline_Endopept 1 P -
70
- 9. Staph_Protease 1 E -
71
- 10. Trypsin_K 1 K P
72
- 11. Trypsin_R 1 R P
73
- 12. GluC 1 ED -
74
- 13. LysC 1 K -
75
- 14. AspN 0 D -
76
- 15. Elastase 1 ALIV P
77
- 16. Elastase/Tryp/Chymo 1 ALIVKRWFY P
data/test_files/opd1/sequest.3.2.params DELETED
@@ -1,62 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\ecoli_K12.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 1.5000
5
- peptide_mass_units = 0 ; 0=amu, 1=mmu, 2=ppm
6
- ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
7
- fragment_ion_tolerance = 1.0000 ; leave at 0.0 unless you have real poor data
8
- num_output_lines = 10 ; # peptide results to show
9
- num_results = 500 ; # results to store
10
- num_description_lines = 5 ; # full protein descriptions to show for top N peptides
11
- show_fragment_ions = 1 ; 0=no, 1=yes
12
- print_duplicate_references = 40 ; 0=no, 1=yes
13
- enzyme_info = Trypsin(KR) 1 1 KR -
14
- max_num_differential_per_peptide = 3 ; max # of diff. mod in a peptide
15
- diff_search_options = 0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y
16
- term_diff_search_options = 0.000000 0.000000
17
- nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
18
- mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
19
- mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
20
- normalize_xcorr = 0 ; use normalized xcorr values in the out file
21
- remove_precursor_peak = 0 ; 0=no, 1=yes
22
- ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
23
- max_num_internal_cleavage_sites = 2 ; maximum value is 5
24
- protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
25
- match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
26
- match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
27
- match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
28
- partial_sequence =
29
- sequence_header_filter =
30
- digest_mass_range = 600.0 3500.0
31
-
32
- add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
33
- add_Cterm_protein = 0.0000 ; added to each protein C-terminus
34
- add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
35
- add_Nterm_protein = 0.0000 ; added to each protein N-terminus
36
- add_G_Glycine = 0.0000 ; added to G - avg. 57.0519, mono. 57.02146
37
- add_A_Alanine = 0.0000 ; added to A - avg. 71.0788, mono. 71.03711
38
- add_S_Serine = 0.0000 ; added to S - avg. 87.0782, mono. 87.02303
39
- add_P_Proline = 0.0000 ; added to P - avg. 97.1167, mono. 97.05276
40
- add_V_Valine = 0.0000 ; added to V - avg. 99.1326, mono. 99.06841
41
- add_T_Threonine = 0.0000 ; added to T - avg. 101.1051, mono. 101.04768
42
- add_C_Cysteine = 0.0000 ; added to C - avg. 103.1388, mono. 103.00919
43
- add_L_Leucine = 0.0000 ; added to L - avg. 113.1594, mono. 113.08406
44
- add_I_Isoleucine = 0.0000 ; added to I - avg. 113.1594, mono. 113.08406
45
- add_X_LorI = 0.0000 ; added to X - avg. 113.1594, mono. 113.08406
46
- add_N_Asparagine = 0.0000 ; added to N - avg. 114.1038, mono. 114.04293
47
- add_O_Ornithine = 0.0000 ; added to O - avg. 114.1472, mono 114.07931
48
- add_B_avg_NandD = 0.0000 ; added to B - avg. 114.5962, mono. 114.53494
49
- add_D_Aspartic_Acid = 0.0000 ; added to D - avg. 115.0886, mono. 115.02694
50
- add_Q_Glutamine = 0.0000 ; added to Q - avg. 128.1307, mono. 128.05858
51
- add_K_Lysine = 0.0000 ; added to K - avg. 128.1741, mono. 128.09496
52
- add_Z_avg_QandE = 0.0000 ; added to Z - avg. 128.6231, mono. 128.55059
53
- add_E_Glutamic_Acid = 0.0000 ; added to E - avg. 129.1155, mono. 129.04259
54
- add_M_Methionine = 0.0000 ; added to M - avg. 131.1926, mono. 131.04049
55
- add_H_Histidine = 0.0000 ; added to H - avg. 137.1411, mono. 137.05891
56
- add_F_Phenylalanine = 0.0000 ; added to F - avg. 147.1766, mono. 147.06841
57
- add_R_Arginine = 0.0000 ; added to R - avg. 156.1875, mono. 156.10111
58
- add_Y_Tyrosine = 0.0000 ; added to Y - avg. 163.1760, mono. 163.06333
59
- add_W_Tryptophan = 0.0000 ; added to W - avg. 186.2132, mono. 186.07931
60
- add_J_user_amino_acid = 0.0000 ; added to J
61
- add_U_user_amino_acid = 0.0000 ; added to U
62
-