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/opd1/000_020-prot.png ADDED
Binary file
data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml ADDED
@@ -0,0 +1,62 @@
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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">
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>
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+ </program_details>
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+ </protein_summary_header>
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+ <dataset_derivation generation_no="0">
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+ </dataset_derivation>
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+ <protein_group group_number="1" probability="1.00">
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+ <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>
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+ </protein>
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+ </protein_group>
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+ <protein_group group_number="2" probability="1.00">
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+ <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 ADDED
@@ -0,0 +1,62 @@
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 ADDED
@@ -0,0 +1,139 @@
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 ADDED
@@ -0,0 +1,77 @@
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 ADDED
@@ -0,0 +1,62 @@
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
+