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
@@ -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
@@ -1,62 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 1.4000
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 ; for trap data leave at 1.0, for accurate mass data use values < 1.0
8
- num_output_lines = 10 ; # peptide results to show
9
- num_results = 250 ; # results to store
10
- num_description_lines = 5 ; # full protein descriptions to show for top N peptides
11
- show_fragment_ions = 0 ; 0=no, 1=yes
12
- print_duplicate_references = 40 ; number of duplicate references reported
13
- enzyme_info = Trypsin(KR/P) 1 1 KR P
14
- max_num_differential_per_peptide = 1 ; 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 12
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
37
- add_A_Alanine = 0.0000 ; added to A
38
- add_S_Serine = 0.0000 ; added to S
39
- add_P_Proline = 0.0000 ; added to P
40
- add_V_Valine = 0.0000 ; added to V
41
- add_T_Threonine = 0.0000 ; added to T
42
- add_C_Cysteine = 0.0000 ; added to C
43
- add_L_Leucine = 0.0000 ; added to L
44
- add_I_Isoleucine = 0.0000 ; added to I
45
- add_X_LorI = 0.0000 ; added to X
46
- add_N_Asparagine = 0.0000 ; added to N
47
- add_O_Ornithine = 0.0000 ; added to O
48
- add_B_avg_NandD = 0.0000 ; added to B
49
- add_D_Aspartic_Acid = 0.0000 ; added to D
50
- add_Q_Glutamine = 0.0000 ; added to Q
51
- add_K_Lysine = 0.0000 ; added to K
52
- add_Z_avg_QandE = 0.0000 ; added to Z
53
- add_E_Glutamic_Acid = 0.0000 ; added to E
54
- add_M_Methionine = 0.0000 ; added to M
55
- add_H_Histidine = 0.0000 ; added to H
56
- add_F_Phenylalanine = 0.0000 ; added to F
57
- add_R_Arginine = 0.0000 ; added to R
58
- add_Y_Tyrosine = 0.0000 ; added to Y
59
- add_W_Tryptophan = 0.0000 ; added to W
60
- add_J_user_amino_acid = 0.0000 ; added to J
61
- add_U_user_amino_acid = 0.0000 ; added to U
62
-
@@ -1,63 +0,0 @@
1
- [SEQUEST]
2
- first_database_name = C:\Xcalibur\database\yeast.fasta
3
- second_database_name =
4
- peptide_mass_tolerance = 2.0000
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 ; for trap data leave at 1.0, for accurate mass data use values < 1.0
8
- fragment_ion_units = 0 ; 0=amu, 1=mmu
9
- num_output_lines = 10 ; # peptide results to show
10
- num_results = 250 ; # results to store
11
- num_description_lines = 5 ; # full protein descriptions to show for top N peptides
12
- show_fragment_ions = 0 ; 0=no, 1=yes
13
- print_duplicate_references = 0 ; number of duplicate references reported
14
- enzyme_info = Trypsin(KR) 1 1 KR -
15
- max_num_differential_per_peptide = 3 ; max # of diff. mod in a peptide
16
- diff_search_options = 0.0000 S 0.0000 C 0.0000 M 0.0000 X 0.0000 T 0.0000 Y
17
- term_diff_search_options = 0.0000 0.0000
18
- nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
19
- mass_type_parent = 1 ; 0=average masses, 1=monoisotopic masses
20
- mass_type_fragment = 1 ; 0=average masses, 1=monoisotopic masses
21
- normalize_xcorr = 0 ; use normalized xcorr values in the out file
22
- remove_precursor_peak = 0 ; 0=no, 1=yes
23
- ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
24
- max_num_internal_cleavage_sites = 2 ; maximum value is 12
25
- protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
26
- match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
27
- match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
28
- match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
29
- partial_sequence =
30
- sequence_header_filter =
31
- digest_mass_range = 600.0000 4500.0000
32
-
33
- add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
34
- add_Cterm_protein = 0.0000 ; added to each protein C-terminus
35
- add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
36
- add_Nterm_protein = 0.0000 ; added to each protein N-terminus
37
- add_G_Glycine = 0.0000 ; added to G
38
- add_A_Alanine = 0.0000 ; added to A
39
- add_S_Serine = 0.0000 ; added to S
40
- add_P_Proline = 0.0000 ; added to P
41
- add_V_Valine = 0.0000 ; added to V
42
- add_T_Threonine = 0.0000 ; added to T
43
- add_C_Cysteine = 0.0000 ; added to C
44
- add_L_Leucine = 0.0000 ; added to L
45
- add_I_Isoleucine = 0.0000 ; added to I
46
- add_X_LorI = 0.0000 ; added to X
47
- add_N_Asparagine = 0.0000 ; added to N
48
- add_O_Ornithine = 0.0000 ; added to O
49
- add_B_avg_NandD = 0.0000 ; added to B
50
- add_D_Aspartic_Acid = 0.0000 ; added to D
51
- add_Q_Glutamine = 0.0000 ; added to Q
52
- add_K_Lysine = 0.0000 ; added to K
53
- add_Z_avg_QandE = 0.0000 ; added to Z
54
- add_E_Glutamic_Acid = 0.0000 ; added to E
55
- add_M_Methionine = 0.0000 ; added to M
56
- add_H_Histidine = 0.0000 ; added to H
57
- add_F_Phenylalanine = 0.0000 ; added to F
58
- add_R_Arginine = 0.0000 ; added to R
59
- add_Y_Tyrosine = 0.0000 ; added to Y
60
- add_W_Tryptophan = 0.0000 ; added to W
61
- add_J_user_amino_acid = 0.0000 ; added to J
62
- add_U_user_amino_acid = 0.0000 ; added to U
63
-