mspire 0.4.9 → 0.5.0
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- data/README +27 -17
- data/changelog.txt +31 -62
- data/lib/ms/calc.rb +32 -0
- data/lib/ms/data/interleaved.rb +60 -0
- data/lib/ms/data/lazy_io.rb +73 -0
- data/lib/ms/data/lazy_string.rb +15 -0
- data/lib/ms/data/simple.rb +59 -0
- data/lib/ms/data/transposed.rb +41 -0
- data/lib/ms/data.rb +57 -0
- data/lib/ms/format/format_error.rb +12 -0
- data/lib/ms/spectrum.rb +25 -384
- data/lib/ms/support/binary_search.rb +126 -0
- data/lib/ms.rb +10 -10
- metadata +38 -350
- data/INSTALL +0 -58
- data/README.rdoc +0 -18
- data/Rakefile +0 -330
- data/bin/aafreqs.rb +0 -23
- data/bin/bioworks2excel.rb +0 -14
- data/bin/bioworks_to_pepxml.rb +0 -148
- data/bin/bioworks_to_pepxml_gui.rb +0 -225
- data/bin/fasta_shaker.rb +0 -5
- data/bin/filter_and_validate.rb +0 -5
- data/bin/gi2annot.rb +0 -14
- data/bin/id_class_anal.rb +0 -112
- data/bin/id_precision.rb +0 -172
- data/bin/ms_to_lmat.rb +0 -67
- data/bin/pepproph_filter.rb +0 -16
- data/bin/prob_validate.rb +0 -6
- data/bin/protein_summary.rb +0 -6
- data/bin/protxml2prots_peps.rb +0 -32
- data/bin/raw_to_mzXML.rb +0 -55
- data/bin/run_percolator.rb +0 -122
- data/bin/sqt_group.rb +0 -26
- data/bin/srf_group.rb +0 -27
- data/bin/srf_to_sqt.rb +0 -40
- data/lib/align/chams.rb +0 -78
- data/lib/align.rb +0 -154
- data/lib/archive/targz.rb +0 -94
- data/lib/bsearch.rb +0 -120
- data/lib/core_extensions.rb +0 -16
- data/lib/fasta.rb +0 -626
- data/lib/gi.rb +0 -124
- data/lib/group_by.rb +0 -10
- data/lib/index_by.rb +0 -11
- data/lib/merge_deep.rb +0 -21
- data/lib/ms/converter/mzxml.rb +0 -77
- data/lib/ms/gradient_program.rb +0 -170
- data/lib/ms/msrun.rb +0 -244
- data/lib/ms/msrun_index.rb +0 -108
- data/lib/ms/parser/mzdata/axml.rb +0 -67
- data/lib/ms/parser/mzdata/dom.rb +0 -175
- data/lib/ms/parser/mzdata/libxml.rb +0 -7
- data/lib/ms/parser/mzdata.rb +0 -31
- data/lib/ms/parser/mzxml/axml.rb +0 -70
- data/lib/ms/parser/mzxml/dom.rb +0 -182
- data/lib/ms/parser/mzxml/hpricot.rb +0 -253
- data/lib/ms/parser/mzxml/libxml.rb +0 -19
- data/lib/ms/parser/mzxml/regexp.rb +0 -122
- data/lib/ms/parser/mzxml/rexml.rb +0 -72
- data/lib/ms/parser/mzxml/xmlparser.rb +0 -248
- data/lib/ms/parser/mzxml.rb +0 -282
- data/lib/ms/parser.rb +0 -108
- data/lib/ms/precursor.rb +0 -25
- data/lib/ms/scan.rb +0 -81
- data/lib/mspire.rb +0 -4
- data/lib/pi_zero.rb +0 -244
- data/lib/qvalue.rb +0 -161
- data/lib/roc.rb +0 -187
- data/lib/sample_enzyme.rb +0 -160
- data/lib/scan_i.rb +0 -21
- data/lib/spec_id/aa_freqs.rb +0 -170
- data/lib/spec_id/bioworks.rb +0 -497
- data/lib/spec_id/digestor.rb +0 -138
- data/lib/spec_id/mass.rb +0 -179
- data/lib/spec_id/parser/proph.rb +0 -335
- data/lib/spec_id/precision/filter/cmdline.rb +0 -218
- data/lib/spec_id/precision/filter/interactive.rb +0 -134
- data/lib/spec_id/precision/filter/output.rb +0 -148
- data/lib/spec_id/precision/filter.rb +0 -637
- data/lib/spec_id/precision/output.rb +0 -60
- data/lib/spec_id/precision/prob/cmdline.rb +0 -160
- data/lib/spec_id/precision/prob/output.rb +0 -94
- data/lib/spec_id/precision/prob.rb +0 -249
- data/lib/spec_id/proph/pep_summary.rb +0 -104
- data/lib/spec_id/proph/prot_summary.rb +0 -484
- data/lib/spec_id/proph.rb +0 -4
- data/lib/spec_id/protein_summary.rb +0 -489
- data/lib/spec_id/sequest/params.rb +0 -316
- data/lib/spec_id/sequest/pepxml.rb +0 -1458
- data/lib/spec_id/sequest.rb +0 -33
- data/lib/spec_id/sqt.rb +0 -349
- data/lib/spec_id/srf.rb +0 -973
- data/lib/spec_id.rb +0 -778
- data/lib/spec_id_xml.rb +0 -99
- data/lib/transmem/phobius.rb +0 -147
- data/lib/transmem/toppred.rb +0 -368
- data/lib/transmem.rb +0 -157
- data/lib/validator/aa.rb +0 -48
- data/lib/validator/aa_est.rb +0 -112
- data/lib/validator/background.rb +0 -77
- data/lib/validator/bias.rb +0 -95
- data/lib/validator/cmdline.rb +0 -431
- data/lib/validator/decoy.rb +0 -107
- data/lib/validator/digestion_based.rb +0 -70
- data/lib/validator/probability.rb +0 -51
- data/lib/validator/prot_from_pep.rb +0 -234
- data/lib/validator/q_value.rb +0 -32
- data/lib/validator/transmem.rb +0 -272
- data/lib/validator/true_pos.rb +0 -46
- data/lib/validator.rb +0 -197
- data/lib/xml.rb +0 -38
- data/lib/xml_style_parser.rb +0 -119
- data/lib/xmlparser_wrapper.rb +0 -19
- data/release_notes.txt +0 -2
- data/script/compile_and_plot_smriti_final.rb +0 -97
- data/script/create_little_pepxml.rb +0 -61
- data/script/degenerate_peptides.rb +0 -47
- data/script/estimate_fpr_by_cysteine.rb +0 -226
- data/script/extract_gradient_programs.rb +0 -56
- data/script/find_cysteine_background.rb +0 -137
- data/script/genuine_tps_and_probs.rb +0 -136
- data/script/get_apex_values_rexml.rb +0 -44
- data/script/histogram_probs.rb +0 -61
- data/script/mascot_fix_pepxml.rb +0 -123
- data/script/msvis.rb +0 -42
- data/script/mzXML2timeIndex.rb +0 -25
- data/script/peps_per_bin.rb +0 -67
- data/script/prep_dir.rb +0 -121
- data/script/simple_protein_digestion.rb +0 -27
- data/script/smriti_final_analysis.rb +0 -103
- data/script/sqt_to_meta.rb +0 -24
- data/script/top_hit_per_scan.rb +0 -67
- data/script/toppred_to_yaml.rb +0 -47
- data/script/tpp_installer.rb +0 -249
- data/specs/align_spec.rb +0 -79
- data/specs/bin/bioworks_to_pepxml_spec.rb +0 -79
- data/specs/bin/fasta_shaker_spec.rb +0 -259
- data/specs/bin/filter_and_validate__multiple_vals_helper.yaml +0 -199
- data/specs/bin/filter_and_validate_spec.rb +0 -180
- data/specs/bin/ms_to_lmat_spec.rb +0 -34
- data/specs/bin/prob_validate_spec.rb +0 -86
- data/specs/bin/protein_summary_spec.rb +0 -14
- data/specs/fasta_spec.rb +0 -354
- data/specs/gi_spec.rb +0 -22
- data/specs/load_bin_path.rb +0 -7
- data/specs/merge_deep_spec.rb +0 -13
- data/specs/ms/gradient_program_spec.rb +0 -77
- data/specs/ms/msrun_spec.rb +0 -498
- data/specs/ms/parser_spec.rb +0 -92
- data/specs/ms/spectrum_spec.rb +0 -87
- data/specs/pi_zero_spec.rb +0 -115
- data/specs/qvalue_spec.rb +0 -39
- data/specs/roc_spec.rb +0 -251
- data/specs/rspec_autotest.rb +0 -149
- data/specs/sample_enzyme_spec.rb +0 -126
- data/specs/spec_helper.rb +0 -135
- data/specs/spec_id/aa_freqs_spec.rb +0 -52
- data/specs/spec_id/bioworks_spec.rb +0 -148
- data/specs/spec_id/digestor_spec.rb +0 -75
- data/specs/spec_id/precision/filter/cmdline_spec.rb +0 -20
- data/specs/spec_id/precision/filter/output_spec.rb +0 -31
- data/specs/spec_id/precision/filter_spec.rb +0 -246
- data/specs/spec_id/precision/prob_spec.rb +0 -44
- data/specs/spec_id/precision/prob_spec_helper.rb +0 -0
- data/specs/spec_id/proph/pep_summary_spec.rb +0 -98
- data/specs/spec_id/proph/prot_summary_spec.rb +0 -128
- data/specs/spec_id/protein_summary_spec.rb +0 -189
- data/specs/spec_id/sequest/params_spec.rb +0 -68
- data/specs/spec_id/sequest/pepxml_spec.rb +0 -374
- data/specs/spec_id/sequest_spec.rb +0 -38
- data/specs/spec_id/sqt_spec.rb +0 -246
- data/specs/spec_id/srf_spec.rb +0 -172
- data/specs/spec_id/srf_spec_helper.rb +0 -139
- data/specs/spec_id_helper.rb +0 -33
- data/specs/spec_id_spec.rb +0 -366
- data/specs/spec_id_xml_spec.rb +0 -33
- data/specs/transmem/phobius_spec.rb +0 -425
- data/specs/transmem/toppred_spec.rb +0 -298
- data/specs/transmem_spec.rb +0 -60
- data/specs/transmem_spec_shared.rb +0 -64
- data/specs/validator/aa_est_spec.rb +0 -66
- data/specs/validator/aa_spec.rb +0 -40
- data/specs/validator/background_spec.rb +0 -67
- data/specs/validator/bias_spec.rb +0 -122
- data/specs/validator/decoy_spec.rb +0 -51
- data/specs/validator/fasta_helper.rb +0 -26
- data/specs/validator/prot_from_pep_spec.rb +0 -141
- data/specs/validator/transmem_spec.rb +0 -146
- data/specs/validator/true_pos_spec.rb +0 -58
- data/specs/validator_helper.rb +0 -33
- data/specs/xml_spec.rb +0 -12
- data/test_files/000_pepxml18_small.xml +0 -206
- data/test_files/020a.mzXML.timeIndex +0 -4710
- data/test_files/4-03-03_mzXML/000.mzXML.timeIndex +0 -3973
- data/test_files/4-03-03_mzXML/020.mzXML.timeIndex +0 -3872
- data/test_files/4-03-03_small-prot.xml +0 -321
- data/test_files/4-03-03_small.xml +0 -3876
- data/test_files/7MIX_STD_110802_1.sequest_params_fragment.srf +0 -0
- data/test_files/bioworks-3.3_10prots.xml +0 -5999
- data/test_files/bioworks31.params +0 -77
- data/test_files/bioworks32.params +0 -62
- data/test_files/bioworks33.params +0 -63
- data/test_files/bioworks_single_run_small.xml +0 -7237
- data/test_files/bioworks_small.fasta +0 -212
- data/test_files/bioworks_small.params +0 -63
- data/test_files/bioworks_small.phobius +0 -109
- data/test_files/bioworks_small.toppred.out +0 -2847
- data/test_files/bioworks_small.xml +0 -5610
- data/test_files/bioworks_with_INV_small.xml +0 -3753
- data/test_files/bioworks_with_SHUFF_small.xml +0 -2503
- 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 +0 -304
- data/test_files/messups.fasta +0 -297
- data/test_files/opd1/000.my_answer.100lines.xml +0 -101
- data/test_files/opd1/000.tpp_1.2.3.first10.xml +0 -115
- data/test_files/opd1/000.tpp_2.9.2.first10.xml +0 -126
- data/test_files/opd1/000.v2.1.mzXML.timeIndex +0 -3748
- data/test_files/opd1/000_020-prot.png +0 -0
- data/test_files/opd1/000_020_3prots-prot.mod_initprob.xml +0 -62
- data/test_files/opd1/000_020_3prots-prot.xml +0 -62
- data/test_files/opd1/opd1_cat_inv_small-prot.xml +0 -139
- data/test_files/opd1/sequest.3.1.params +0 -77
- data/test_files/opd1/sequest.3.2.params +0 -62
- data/test_files/opd1/twenty_scans.mzXML +0 -418
- data/test_files/opd1/twenty_scans.v2.1.mzXML +0 -382
- data/test_files/opd1/twenty_scans_answ.lmat +0 -0
- data/test_files/opd1/twenty_scans_answ.lmata +0 -9
- data/test_files/opd1_020_beginning.RAW +0 -0
- data/test_files/opd1_2runs_2mods/data/020.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/040.mzData.xml +0 -683
- data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +0 -382
- data/test_files/opd1_2runs_2mods/data/README.txt +0 -6
- data/test_files/opd1_2runs_2mods/interact-opd1_mods__small.xml +0 -753
- data/test_files/orbitrap_mzData/000_cut.xml +0 -1920
- data/test_files/pepproph_small.xml +0 -4691
- data/test_files/phobius.small.noheader.txt +0 -50
- data/test_files/phobius.small.small.txt +0 -53
- data/test_files/s01_anC1_ld020mM.key.txt +0 -25
- data/test_files/s01_anC1_ld020mM.meth +0 -0
- data/test_files/small.fasta +0 -297
- data/test_files/small.sqt +0 -87
- data/test_files/smallraw.RAW +0 -0
- data/test_files/tf_bioworks2excel.bioXML +0 -14340
- data/test_files/tf_bioworks2excel.txt.actual +0 -1035
- data/test_files/toppred.small.out +0 -416
- data/test_files/toppred.xml.out +0 -318
- data/test_files/validator_hits_separate/bias_bioworks_small_HS.fasta +0 -7
- data/test_files/validator_hits_separate/bioworks_small_HS.xml +0 -5651
- data/test_files/yeast_gly_small-prot.xml +0 -265
- data/test_files/yeast_gly_small.1.0_1.0_1.0.parentTimes +0 -6
- data/test_files/yeast_gly_small.xml +0 -3807
- data/test_files/yeast_gly_small2.parentTimes +0 -6
@@ -1,77 +0,0 @@
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[SEQUEST]
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first_database_name = C:\Xcalibur\database\ecoli_K12.fasta
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second_database_name =
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peptide_mass_tolerance = 1.5000
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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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fragment_ion_tolerance = 0.0000 ; leave at 0.0 unless you have real poor data
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num_output_lines = 10 ; # peptide results to show
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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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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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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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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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add_X_LorI = 0.0000 ; added to X - avg. 113.1594, mono. 113.08406
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add_N_Asparagine = 0.0000 ; added to N - avg. 114.1038, mono. 114.04293
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add_O_Ornithine = 0.0000 ; added to O - avg. 114.1472, mono 114.07931
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add_B_avg_NandD = 0.0000 ; added to B - avg. 114.5962, mono. 114.53494
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add_D_Aspartic_Acid = 0.0000 ; added to D - avg. 115.0886, mono. 115.02694
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add_Q_Glutamine = 0.0000 ; added to Q - avg. 128.1307, mono. 128.05858
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add_K_Lysine = 0.0000 ; added to K - avg. 128.1741, mono. 128.09496
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add_Z_avg_QandE = 0.0000 ; added to Z - avg. 128.6231, mono. 128.55059
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add_E_Glutamic_Acid = 0.0000 ; added to E - avg. 129.1155, mono. 129.04259
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add_M_Methionine = 0.0000 ; added to M - avg. 131.1926, mono. 131.04049
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add_H_Histidine = 0.0000 ; added to H - avg. 137.1411, mono. 137.05891
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add_F_Phenylalanine = 0.0000 ; added to F - avg. 147.1766, mono. 147.06841
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add_R_Arginine = 0.0000 ; added to R - avg. 156.1875, mono. 156.10111
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add_Y_Tyrosine = 0.0000 ; added to Y - avg. 163.1760, mono. 163.06333
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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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8. Proline_Endopept 1 P -
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9. Staph_Protease 1 E -
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10. Trypsin_K 1 K P
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11. Trypsin_R 1 R P
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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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16. Elastase/Tryp/Chymo 1 ALIVKRWFY P
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@@ -1,62 +0,0 @@
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[SEQUEST]
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first_database_name = C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta
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second_database_name =
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peptide_mass_tolerance = 1.4000
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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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|
-
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
|
-
|