mspire 0.2.4 → 0.3.0
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- data/INSTALL +1 -0
- data/README +25 -0
- data/Rakefile +129 -40
- data/bin/{find_aa_freq.rb → aafreqs.rb} +2 -2
- data/bin/bioworks_to_pepxml.rb +1 -0
- data/bin/fasta_shaker.rb +1 -96
- data/bin/filter_and_validate.rb +5 -0
- data/bin/{mzxml_to_lmat.rb → ms_to_lmat.rb} +8 -7
- data/bin/prob_validate.rb +6 -0
- data/bin/raw_to_mzXML.rb +2 -2
- data/bin/srf_group.rb +1 -0
- data/bin/srf_to_sqt.rb +40 -0
- data/changelog.txt +68 -0
- data/lib/align/chams.rb +6 -6
- data/lib/align.rb +4 -3
- data/lib/bsearch.rb +120 -0
- data/lib/fasta.rb +318 -86
- data/lib/group_by.rb +10 -0
- data/lib/index_by.rb +11 -0
- data/lib/merge_deep.rb +21 -0
- data/lib/{spec → ms/converter}/mzxml.rb +77 -109
- data/lib/ms/gradient_program.rb +171 -0
- data/lib/ms/msrun.rb +209 -0
- data/lib/{spec/msrun.rb → ms/msrun_index.rb} +7 -40
- data/lib/ms/parser/mzdata/axml.rb +12 -0
- data/lib/ms/parser/mzdata/dom.rb +160 -0
- data/lib/ms/parser/mzdata/libxml.rb +7 -0
- data/lib/ms/parser/mzdata.rb +25 -0
- data/lib/ms/parser/mzxml/axml.rb +11 -0
- data/lib/ms/parser/mzxml/dom.rb +159 -0
- data/lib/ms/parser/mzxml/hpricot.rb +253 -0
- data/lib/ms/parser/mzxml/libxml.rb +15 -0
- data/lib/ms/parser/mzxml/regexp.rb +122 -0
- data/lib/ms/parser/mzxml/rexml.rb +72 -0
- data/lib/ms/parser/mzxml/xmlparser.rb +248 -0
- data/lib/ms/parser/mzxml.rb +175 -0
- data/lib/ms/parser.rb +108 -0
- data/lib/ms/precursor.rb +10 -0
- data/lib/ms/scan.rb +81 -0
- data/lib/ms/spectrum.rb +193 -0
- data/lib/ms.rb +10 -0
- data/lib/mspire.rb +4 -0
- data/lib/roc.rb +61 -1
- data/lib/sample_enzyme.rb +31 -8
- data/lib/scan_i.rb +21 -0
- data/lib/spec_id/aa_freqs.rb +7 -3
- data/lib/spec_id/bioworks.rb +20 -14
- data/lib/spec_id/digestor.rb +139 -0
- data/lib/spec_id/mass.rb +116 -0
- data/lib/spec_id/parser/proph.rb +236 -0
- data/lib/spec_id/precision/filter/cmdline.rb +209 -0
- data/lib/spec_id/precision/filter/interactive.rb +134 -0
- data/lib/spec_id/precision/filter/output.rb +147 -0
- data/lib/spec_id/precision/filter.rb +623 -0
- data/lib/spec_id/precision/output.rb +60 -0
- data/lib/spec_id/precision/prob/cmdline.rb +139 -0
- data/lib/spec_id/precision/prob/output.rb +88 -0
- data/lib/spec_id/precision/prob.rb +171 -0
- data/lib/spec_id/proph/pep_summary.rb +92 -0
- data/lib/spec_id/proph/prot_summary.rb +484 -0
- data/lib/spec_id/proph.rb +2 -466
- data/lib/spec_id/protein_summary.rb +2 -2
- data/lib/spec_id/sequest/params.rb +316 -0
- data/lib/spec_id/sequest/pepxml.rb +1513 -0
- data/lib/spec_id/sequest.rb +2 -1672
- data/lib/spec_id/srf.rb +445 -177
- data/lib/spec_id.rb +183 -95
- data/lib/spec_id_xml.rb +8 -10
- data/lib/transmem/phobius.rb +147 -0
- data/lib/transmem/toppred.rb +368 -0
- data/lib/transmem.rb +157 -0
- data/lib/validator/aa.rb +135 -0
- data/lib/validator/background.rb +73 -0
- data/lib/validator/bias.rb +95 -0
- data/lib/validator/cmdline.rb +260 -0
- data/lib/validator/decoy.rb +94 -0
- data/lib/validator/digestion_based.rb +69 -0
- data/lib/validator/probability.rb +48 -0
- data/lib/validator/prot_from_pep.rb +234 -0
- data/lib/validator/transmem.rb +272 -0
- data/lib/validator/true_pos.rb +46 -0
- data/lib/validator.rb +214 -0
- data/lib/xml.rb +38 -0
- data/lib/xml_style_parser.rb +105 -0
- data/lib/xmlparser_wrapper.rb +19 -0
- data/script/compile_and_plot_smriti_final.rb +97 -0
- data/script/extract_gradient_programs.rb +56 -0
- data/script/get_apex_values_rexml.rb +44 -0
- data/script/mzXML2timeIndex.rb +1 -1
- data/script/smriti_final_analysis.rb +103 -0
- data/script/toppred_to_yaml.rb +47 -0
- data/script/tpp_installer.rb +1 -1
- data/{test/tc_align.rb → specs/align_spec.rb} +21 -27
- data/{test/tc_bioworks_to_pepxml.rb → specs/bin/bioworks_to_pepxml_spec.rb} +25 -41
- data/specs/bin/fasta_shaker_spec.rb +259 -0
- data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +202 -0
- data/specs/bin/filter_and_validate_spec.rb +124 -0
- data/specs/bin/ms_to_lmat_spec.rb +34 -0
- data/specs/bin/prob_validate_spec.rb +62 -0
- data/specs/bin/protein_summary_spec.rb +10 -0
- data/{test/tc_fasta.rb → specs/fasta_spec.rb} +354 -310
- data/specs/gi_spec.rb +22 -0
- data/specs/load_bin_path.rb +7 -0
- data/specs/merge_deep_spec.rb +13 -0
- data/specs/ms/gradient_program_spec.rb +77 -0
- data/specs/ms/msrun_spec.rb +455 -0
- data/specs/ms/parser_spec.rb +92 -0
- data/specs/ms/spectrum_spec.rb +89 -0
- data/specs/roc_spec.rb +251 -0
- data/specs/rspec_autotest.rb +149 -0
- data/specs/sample_enzyme_spec.rb +41 -0
- data/specs/spec_helper.rb +133 -0
- data/specs/spec_id/aa_freqs_spec.rb +52 -0
- data/{test/tc_bioworks.rb → specs/spec_id/bioworks_spec.rb} +56 -71
- data/specs/spec_id/digestor_spec.rb +75 -0
- data/specs/spec_id/precision/filter/cmdline_spec.rb +20 -0
- data/specs/spec_id/precision/filter/output_spec.rb +31 -0
- data/specs/spec_id/precision/filter_spec.rb +243 -0
- data/specs/spec_id/precision/prob_spec.rb +111 -0
- data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
- data/specs/spec_id/proph/pep_summary_spec.rb +143 -0
- data/{test/tc_proph.rb → specs/spec_id/proph/prot_summary_spec.rb} +52 -32
- data/{test/tc_protein_summary.rb → specs/spec_id/protein_summary_spec.rb} +85 -0
- data/specs/spec_id/sequest/params_spec.rb +68 -0
- data/specs/spec_id/sequest/pepxml_spec.rb +452 -0
- data/specs/spec_id/sqt_spec.rb +138 -0
- data/specs/spec_id/srf_spec.rb +209 -0
- data/specs/spec_id/srf_spec_helper.rb +302 -0
- data/specs/spec_id_helper.rb +33 -0
- data/specs/spec_id_spec.rb +361 -0
- data/specs/spec_id_xml_spec.rb +33 -0
- data/specs/transmem/phobius_spec.rb +423 -0
- data/specs/transmem/toppred_spec.rb +297 -0
- data/specs/transmem_spec.rb +60 -0
- data/specs/transmem_spec_shared.rb +64 -0
- data/specs/validator/aa_spec.rb +107 -0
- data/specs/validator/background_spec.rb +51 -0
- data/specs/validator/bias_spec.rb +146 -0
- data/specs/validator/decoy_spec.rb +51 -0
- data/specs/validator/fasta_helper.rb +26 -0
- data/specs/validator/prot_from_pep_spec.rb +141 -0
- data/specs/validator/transmem_spec.rb +145 -0
- data/specs/validator/true_pos_spec.rb +58 -0
- data/specs/validator_helper.rb +33 -0
- data/specs/xml_spec.rb +12 -0
- data/test_files/000_pepxml18_small.xml +206 -0
- data/test_files/020a.mzXML.timeIndex +4710 -0
- data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +3973 -0
- data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +3872 -0
- data/test_files/4-03-03_small-prot.xml +321 -0
- data/test_files/4-03-03_small.xml +3876 -0
- data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
- data/test_files/bioworks-3.3_10prots.xml +5999 -0
- data/test_files/bioworks31.params +77 -0
- data/test_files/bioworks32.params +62 -0
- data/test_files/bioworks33.params +63 -0
- data/test_files/bioworks_single_run_small.xml +7237 -0
- data/test_files/bioworks_small.fasta +212 -0
- data/test_files/bioworks_small.params +63 -0
- data/test_files/bioworks_small.phobius +109 -0
- data/test_files/bioworks_small.toppred.out +2847 -0
- data/test_files/bioworks_small.xml +5610 -0
- data/test_files/bioworks_with_INV_small.xml +3753 -0
- data/test_files/bioworks_with_SHUFF_small.xml +2503 -0
- data/test_files/corrupted_900.srf +0 -0
- data/test_files/head_of_7MIX.srf +0 -0
- data/test_files/interact-opd1_mods_small-prot.xml +304 -0
- data/test_files/messups.fasta +297 -0
- data/test_files/opd1/000.my_answer.100lines.xml +101 -0
- data/test_files/opd1/000.tpp_1.2.3.first10.xml +115 -0
- data/test_files/opd1/000.tpp_2.9.2.first10.xml +126 -0
- data/test_files/opd1/000.v2.1.mzXML.timeIndex +3748 -0
- data/test_files/opd1/000_020-prot.png +0 -0
- data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +62 -0
- data/test_files/opd1/000_020_3prots-prot.xml +62 -0
- data/test_files/opd1/opd1_cat_inv_small-prot.xml +139 -0
- data/test_files/opd1/sequest.3.1.params +77 -0
- data/test_files/opd1/sequest.3.2.params +62 -0
- data/test_files/opd1/twenty_scans.mzXML +418 -0
- data/test_files/opd1/twenty_scans.v2.1.mzXML +382 -0
- data/test_files/opd1/twenty_scans_answ.lmat +0 -0
- data/test_files/opd1/twenty_scans_answ.lmata +9 -0
- data/test_files/opd1_020_beginning.RAW +0 -0
- data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +753 -0
- data/test_files/orbitrap_mzData/000_cut.xml +1920 -0
- data/test_files/pepproph_small.xml +4691 -0
- data/test_files/phobius.small.noheader.txt +50 -0
- data/test_files/phobius.small.small.txt +53 -0
- data/test_files/s01_anC1_ld020mM.key.txt +25 -0
- data/test_files/s01_anC1_ld020mM.meth +0 -0
- data/test_files/small.fasta +297 -0
- data/test_files/smallraw.RAW +0 -0
- data/test_files/tf_bioworks2excel.bioXML +14340 -0
- data/test_files/tf_bioworks2excel.txt.actual +1035 -0
- data/test_files/toppred.small.out +416 -0
- data/test_files/toppred.xml.out +318 -0
- data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +7 -0
- data/test_files/validator_hits_separate/bioworks_small_HS.xml +5651 -0
- data/test_files/yeast_gly_small-prot.xml +265 -0
- data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +6 -0
- data/test_files/yeast_gly_small.xml +3807 -0
- data/test_files/yeast_gly_small2.parentTimes +6 -0
- metadata +273 -57
- data/bin/filter.rb +0 -6
- data/bin/precision.rb +0 -5
- data/lib/spec/mzdata/parser.rb +0 -108
- data/lib/spec/mzdata.rb +0 -48
- data/lib/spec/mzxml/parser.rb +0 -449
- data/lib/spec/scan.rb +0 -55
- data/lib/spec_id/filter.rb +0 -797
- data/lib/spec_id/precision.rb +0 -421
- data/lib/toppred.rb +0 -18
- data/script/filter-peps.rb +0 -164
- data/test/tc_aa_freqs.rb +0 -59
- data/test/tc_fasta_shaker.rb +0 -149
- data/test/tc_filter.rb +0 -203
- data/test/tc_filter_peps.rb +0 -46
- data/test/tc_gi.rb +0 -17
- data/test/tc_id_class_anal.rb +0 -70
- data/test/tc_id_precision.rb +0 -89
- data/test/tc_msrun.rb +0 -88
- data/test/tc_mzxml.rb +0 -88
- data/test/tc_mzxml_to_lmat.rb +0 -36
- data/test/tc_peptide_parent_times.rb +0 -27
- data/test/tc_precision.rb +0 -60
- data/test/tc_roc.rb +0 -166
- data/test/tc_sample_enzyme.rb +0 -32
- data/test/tc_scan.rb +0 -26
- data/test/tc_sequest.rb +0 -336
- data/test/tc_spec.rb +0 -78
- data/test/tc_spec_id.rb +0 -201
- data/test/tc_spec_id_xml.rb +0 -36
- data/test/tc_srf.rb +0 -262
@@ -0,0 +1,77 @@
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[SEQUEST]
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first_database_name = C:\Xcalibur\database\ecoli_K12.fasta
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3
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second_database_name =
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4
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peptide_mass_tolerance = 1.5000
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5
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ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
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6
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fragment_ion_tolerance = 0.0000 ; leave at 0.0 unless you have real poor data
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7
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num_output_lines = 10 ; # peptide results to show
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8
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num_results = 500 ; # results to store
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num_description_lines = 5 ; # full protein descriptions to show for top N peptides
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show_fragment_ions = 1 ; 0=no, 1=yes
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print_duplicate_references = 40 ; 0=no, 1=yes
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enzyme_number = 1
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max_num_differential_AA_per_mod = 4 ; max # of modified AA per diff. mod in a peptide
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14
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diff_search_options = 0.0000 S 0.0000 C 0.0000 M 0.0000 X 0.0000 T 0.0000 Y
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15
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term_diff_search_options = 0.0000 0.0000
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nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
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mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
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mass_type_fragment = 0 ; 0=average masses, 1=monoisotopic masses
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normalize_xcorr = 0 ; use normalized xcorr values in the out file
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remove_precursor_peak = 0 ; 0=no, 1=yes
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ion_cutoff_percentage = 0.0000 ; prelim. score cutoff % as a decimal number i.e. 0.30 for 30%
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max_num_internal_cleavage_sites = 2 ; maximum value is 5
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protein_mass_filter = 0 0 ; enter protein mass min & max value ( 0 for both = unused)
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match_peak_count = 0 ; number of auto-detected peaks to try matching (max 5)
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match_peak_allowed_error = 1 ; number of allowed errors in matching auto-detected peaks
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match_peak_tolerance = 1.0000 ; mass tolerance for matching auto-detected peaks
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create_output_files = 1 ; 0=no, 1=yes
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partial_sequence =
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sequence_header_filter =
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add_Cterm_peptide = 0.0000 ; added to each peptide C-terminus
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add_Cterm_protein = 0.0000 ; added to each protein C-terminus
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add_Nterm_peptide = 0.0000 ; added to each peptide N-terminus
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add_Nterm_protein = 0.0000 ; added to each protein N-terminus
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add_G_Glycine = 0.0000 ; added to G - avg. 57.0519, mono. 57.02146
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add_A_Alanine = 0.0000 ; added to A - avg. 71.0788, mono. 71.03711
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add_S_Serine = 0.0000 ; added to S - avg. 87.0782, mono. 87.02303
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add_P_Proline = 0.0000 ; added to P - avg. 97.1167, mono. 97.05276
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add_V_Valine = 0.0000 ; added to V - avg. 99.1326, mono. 99.06841
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40
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add_T_Threonine = 0.0000 ; added to T - avg. 101.1051, mono. 101.04768
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add_C_Cysteine = 0.0000 ; added to C - avg. 103.1388, mono. 103.00919
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add_L_Leucine = 0.0000 ; added to L - avg. 113.1594, mono. 113.08406
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add_I_Isoleucine = 0.0000 ; added to I - avg. 113.1594, mono. 113.08406
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44
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add_X_LorI = 0.0000 ; added to X - avg. 113.1594, mono. 113.08406
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45
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add_N_Asparagine = 0.0000 ; added to N - avg. 114.1038, mono. 114.04293
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46
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add_O_Ornithine = 0.0000 ; added to O - avg. 114.1472, mono 114.07931
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47
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add_B_avg_NandD = 0.0000 ; added to B - avg. 114.5962, mono. 114.53494
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48
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add_D_Aspartic_Acid = 0.0000 ; added to D - avg. 115.0886, mono. 115.02694
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49
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add_Q_Glutamine = 0.0000 ; added to Q - avg. 128.1307, mono. 128.05858
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50
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add_K_Lysine = 0.0000 ; added to K - avg. 128.1741, mono. 128.09496
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51
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add_Z_avg_QandE = 0.0000 ; added to Z - avg. 128.6231, mono. 128.55059
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52
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add_E_Glutamic_Acid = 0.0000 ; added to E - avg. 129.1155, mono. 129.04259
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53
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add_M_Methionine = 0.0000 ; added to M - avg. 131.1926, mono. 131.04049
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54
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add_H_Histidine = 0.0000 ; added to H - avg. 137.1411, mono. 137.05891
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55
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add_F_Phenylalanine = 0.0000 ; added to F - avg. 147.1766, mono. 147.06841
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56
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add_R_Arginine = 0.0000 ; added to R - avg. 156.1875, mono. 156.10111
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57
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add_Y_Tyrosine = 0.0000 ; added to Y - avg. 163.1760, mono. 163.06333
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58
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add_W_Tryptophan = 0.0000 ; added to W - avg. 186.2132, mono. 186.07931
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[SEQUEST_ENZYME_INFO]
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0. No_Enzyme 0 - -
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1. Trypsin 1 KR -
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2. Trypsin(KRLNH) 1 KRLNH -
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3. Chymotrypsin 1 FWYL -
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4. Chymotrypsin(FWY) 1 FWY P
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5. Clostripain 1 R -
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6. Cyanogen_Bromide 1 M -
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7. IodosoBenzoate 1 W -
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69
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8. Proline_Endopept 1 P -
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70
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9. Staph_Protease 1 E -
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71
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10. Trypsin_K 1 K P
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72
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11. Trypsin_R 1 R P
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73
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12. GluC 1 ED -
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13. LysC 1 K -
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14. AspN 0 D -
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15. Elastase 1 ALIV P
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77
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16. Elastase/Tryp/Chymo 1 ALIVKRWFY P
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@@ -0,0 +1,62 @@
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[SEQUEST]
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2
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first_database_name = C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
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3
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second_database_name =
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4
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peptide_mass_tolerance = 1.4000
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5
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peptide_mass_units = 0 ; 0=amu, 1=mmu, 2=ppm
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ion_series = 0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0
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7
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fragment_ion_tolerance = 1.0000 ; for trap data leave at 1.0, for accurate mass data use values < 1.0
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num_output_lines = 10 ; # peptide results to show
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9
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num_results = 250 ; # results to store
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10
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num_description_lines = 5 ; # full protein descriptions to show for top N peptides
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11
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show_fragment_ions = 0 ; 0=no, 1=yes
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print_duplicate_references = 40 ; number of duplicate references reported
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enzyme_info = Trypsin(KR/P) 1 1 KR P
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max_num_differential_per_peptide = 1 ; max # of diff. mod in a peptide
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15
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diff_search_options = 0.000000 S 0.000000 C 0.000000 M 0.000000 X 0.000000 T 0.000000 Y
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16
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term_diff_search_options = 0.000000 0.000000
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nucleotide_reading_frame = 0 ; 0=protein db, 1-6, 7 = forward three, 8-reverse three, 9=all six
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mass_type_parent = 0 ; 0=average masses, 1=monoisotopic masses
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|
+
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
|
+
|
@@ -0,0 +1,63 @@
|
|
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
|
+
|