From daa6134f98ff65c2b34d3e5ad144bb28c14a959f Mon Sep 17 00:00:00 2001 From: mukul-kandwal Date: Tue, 3 Jun 2025 14:34:56 -0400 Subject: [PATCH 1/5] changed msfragger_style_4 to work with msfragger 4.2 --- jsons/parameters.json | 587 ++++++++++++++++++++++++++++++++++++++++-- jsons/styles.json | 8 + 2 files changed, 580 insertions(+), 15 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index 61a3227..4c4c7fc 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -6,6 +6,7 @@ "msfragger_style_1": "-Xmx", "msfragger_style_2": "-Xmx", "msfragger_style_3": "-Xmx", + "msfragger_style_4": "-Xmx", "msgfplus_style_1": "-Xmx", "mzidentml_style_1": "-Xmx", "pipi_style_1": "-Xmx", @@ -182,6 +183,7 @@ "mascot_style_1": "add_unimod_default_file", "msamanda_style_1": "add_unimod_default_file", "msfragger_style_3": "add_unimod_default_file", + "msfragger_style_4": "add_unimod_default_file", "msgfplus_style_1": "add_unimod_default_file", "novor_style_1": "add_unimod_default_file", "omssa_style_1": "add_unimod_default_file", @@ -572,6 +574,7 @@ "msfragger_style_1": "allow_multiple_variable_mods_on_residue", "msfragger_style_2": "allow_multiple_variable_mods_on_residue", "msfragger_style_3": "allow_multiple_variable_mods_on_residue", + "msfragger_style_4": "allow_multiple_variable_mods_on_residue", "ursgal_style_1": "allow_multiple_variable_mods_on_residue" }, "name": "allow_multiple_variable_mods_on_residue", @@ -620,6 +623,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] + ], "ursgal_style_1": [ [ false, @@ -3079,11 +3092,12 @@ "value_type": "bool" }, { - "default_value": false, - "description": " Perform mass calibration ", + "default_value": "off", + "description": " Perform mass calibration; select one of: 'off', 'on', 'on and find optimal parameters', 'on and find the optimal fragment mass tolerance'", "key_translations": { "msfragger_style_2": "calibrate_mass", "msfragger_style_3": "calibrate_mass", + "msfragger_style_4": "calibrate_mass", "ursgal_style_1": "calibrate_mass" }, "name": "calibrate_mass", @@ -3095,36 +3109,62 @@ "value_translations": { "msfragger_style_2": [ [ - false, + "off", 0 ], [ - true, + "on", 1 ] ], "msfragger_style_3": [ [ - false, + "off", 0 ], [ - true, + "on", 1 ] ], + "msfragger_style_4": [ + [ + "off", + 0 + ], + [ + "on", + 1 + ], + [ + "on and find optimal parameters", + 2 + ], + [ + "on and find the optimal fragment mass tolerance", + 4 + ] + ], "ursgal_style_1": [ [ - false, - false + "off", + "off" ], [ - true, - true + "on", + "on" + ], + [ + "on and find optimal parameters", + "on and find optimal parameters" + ], + [ + "on and find the optimal fragment mass tolerance", + "on and find the optimal fragment mass tolerance" ] ] }, - "value_type": "bool" + "value_type": "select" }, { "default_value": 0, @@ -3213,6 +3253,7 @@ "msfragger_style_1": "clip_nTerm_M", "msfragger_style_2": "clip_nTerm_M", "msfragger_style_3": "clip_nTerm_M", + "msfragger_style_4": "clip_nTerm_M", "msgfplus_style_1": "-ignoreMetCleavage", "ursgal_style_1": "clip_nterm_m" }, @@ -3300,6 +3341,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] + ], "msgfplus_style_1": [ [ false, @@ -4177,6 +4228,7 @@ "msfragger_style_1": "num_threads", "msfragger_style_2": "num_threads", "msfragger_style_3": "num_threads", + "msfragger_style_4": "num_threads", "msgfplus_style_1": "-thread", "myrimatch_style_1": "-cpus", "omssa_style_1": "-nt", @@ -4262,6 +4314,12 @@ "max - 1" ] ], + "msfragger_style_4": [ + [ + -1, + "max - 1" + ] + ], "msgfplus_style_1": [ [ -1, @@ -4402,6 +4460,7 @@ "msfragger_style_1": "database_name", "msfragger_style_2": "database_name", "msfragger_style_3": "database_name", + "msfragger_style_4": "database_name", "msgfplus_style_1": "-d", "myrimatch_style_1": "ProteinDatabase", "omssa_style_1": "-d", @@ -4559,6 +4618,7 @@ "kojak_style_1": "decoy_tag", "msfragger_style_2": "decoy_prefix", "msfragger_style_3": "decoy_prefix", + "msfragger_style_4": "decoy_prefix", "msgfplus_style_1": "-decoy", "myrimatch_style_1": "DecoyPrefix", "mzidentml_style_1": "-decoyRegex", @@ -4767,6 +4827,7 @@ "key_translations": { "msamanda_style_1": "PerformDeisotoping", "msfragger_style_3": "deisotope", + "msfragger_style_4": "deisotope", "ursgal_style_1": "deisotope_spec" }, "name": "deisotope_spec", @@ -4799,6 +4860,20 @@ 2 ] ], + "msfragger_style_4": [ + [ + "deisotope_with_singleton_charge_one", + 1 + ], + [ + "none", + 0 + ], + [ + "perform_deisotoping", + 2 + ] + ], "ursgal_style_1": [ [ "none", @@ -4857,6 +4932,7 @@ "description": " The given mass range is excluded from searching for shifted ions. ", "key_translations": { "msfragger_style_3": "delta_mass_exclude_ranges", + "msfragger_style_4": "delta_mass_exclude_ranges", "ursgal_style_1": "delta_mass_exclude_range" }, "name": "delta_mass_exclude_range", @@ -4873,6 +4949,7 @@ "description": "Only used in MSFragger labile mode, specifies which amino acids are allowed to contain a labile modification", "key_translations": { "msfragger_style_3": "deltamass_allowed_residues", + "msfragger_style_4": "deltamass_allowed_residues", "ursgal_style_1": "deltamass_allowed_residues" }, "name": "deltamass_allowed_residues", @@ -4887,6 +4964,12 @@ 0 ] ], + "msfragger_style_4": [ + [ + "", + 0 + ] + ], "ursgal_style_1": [ [ "", @@ -5040,6 +5123,7 @@ "description": "Specify molecules (or masses) that will be used as diagnostic fragments in the search. Assuming a charge of 1, the mass of a proton is added to all molecules (and masses). Specify as a dictionary with the keys \"chemical_formulas\", \"unimods\", \"glycans\", \"masses\", and lists with the corresponding molecules as values.", "key_translations": { "msfragger_style_3": "diagnostic_fragments", + "msfragger_style_4": "diagnostic_fragments", "ursgal_style_1": "diagnostic_fragments" }, "name": "diagnostic_fragments", @@ -5323,6 +5407,7 @@ "msfragger_style_1": "enzyme", "msfragger_style_2": "enzyme", "msfragger_style_3": "enzyme", + "msfragger_style_4": "enzyme", "msgfplus_style_1": "-e", "myrimatch_style_1": "CleavageRules", "novor_style_1": "enzyme", @@ -6125,6 +6210,104 @@ "KR;C;" ] ], + "msfragger_style_4": [ + [ + "argc", + "R;C;P" + ], + [ + "aspn", + "D;N;" + ], + [ + "chymotrypsin", + "FMWY;C;P" + ], + [ + "chymotrypsin_p", + "FMWY;C;" + ], + [ + "clostripain", + "R;C;" + ], + [ + "cnbr", + "M;C;P" + ], + [ + "elastase", + "AGILV;C;P" + ], + [ + "formic_acid", + "D;C;P" + ], + [ + "gluc", + "DE;C;P" + ], + [ + "gluc_bicarb", + "E;C;P" + ], + [ + "iodosobenzoate", + "W;C;" + ], + [ + "lysc", + "K;C;P" + ], + [ + "lysc_gluc", + "DEK;C;P" + ], + [ + "lysc_p", + "K;C;" + ], + [ + "lysn", + "K;N;" + ], + [ + "lysn_promisc", + "AKRS;N;" + ], + [ + "nonspecific", + "ACDEFGHIKLMNPQRSTVWY;C;" + ], + [ + "pepsina", + "FL;C;" + ], + [ + "protein_endopeptidase", + "P;C;" + ], + [ + "staph_protease", + "E;C;" + ], + [ + "trypsin", + "KR;C;P" + ], + [ + "trypsin_cnbr", + "KRM;C;P" + ], + [ + "trypsin_gluc", + "DEKR;C;P" + ], + [ + "trypsin_p", + "KR;C;" + ] + ], "msgfplus_style_1": [ [ "alpha_lp", @@ -7032,6 +7215,7 @@ "msfragger_style_1": "num_enzyme_termini", "msfragger_style_2": "num_enzyme_termini", "msfragger_style_3": "num_enzyme_termini", + "msfragger_style_4": "num_enzyme_termini", "msgfplus_style_1": "-ntt", "myrimatch_style_1": "MinTerminiCleavages", "omssa_style_1": "semi_enzyme", @@ -7115,6 +7299,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + "full", + 2 + ], + [ + "semi", + 1 + ] + ], "msgfplus_style_1": [ [ "full", @@ -7963,6 +8157,7 @@ "msfragger_style_1": "clear_mz_range", "msfragger_style_2": "clear_mz_range", "msfragger_style_3": "clear_mz_range", + "msfragger_style_4": "clear_mz_range", "pipi_style_1": "frag_clear_mz_range", "ursgal_style_1": "frag_clear_mz_range" }, @@ -7990,6 +8185,7 @@ "msfragger_style_1": "fragment_mass_tolerance", "msfragger_style_2": "fragment_mass_tolerance", "msfragger_style_3": "fragment_mass_tolerance", + "msfragger_style_4": "fragment_mass_tolerance", "novor_style_1": "fragmentIonErrorTol_part1", "omssa_style_1": "-to", "pepnovo_style_1": "-fragment_tolerance", @@ -8020,6 +8216,7 @@ "msfragger_style_1": "fragment_mass_units", "msfragger_style_2": "fragment_mass_units", "msfragger_style_3": "fragment_mass_units", + "msfragger_style_4": "fragment_mass_units", "novor_style_1": "fragmentIonErrorTol_part2", "omssa_style_1": "frag_mass_tolerance_unit", "pepnovo_style_1": "frag_mass_tolerance_unit", @@ -8080,6 +8277,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + "da", + 0 + ], + [ + "ppm", + 1 + ] + ], "omssa_style_1": [ [ "da", @@ -8188,6 +8395,7 @@ "msfragger_style_1": "max_fragment_charge", "msfragger_style_2": "max_fragment_charge", "msfragger_style_3": "max_fragment_charge", + "msfragger_style_4": "max_fragment_charge", "omssa_style_1": "-zoh", "ursgal_style_1": "frag_max_charge" }, @@ -8225,6 +8433,7 @@ "key_translations": { "comet_style_1": "activation_method", "msfragger_style_3": "activation_types", + "msfragger_style_4": "activation_types", "msgfplus_style_1": "-m", "novor_style_1": "fragmentation", "pnovo_style_1": "activation_type", @@ -8298,6 +8507,28 @@ "HCD" ] ], + "msfragger_style_4": [ + [ + "all", + "all" + ], + [ + "cid", + "CID" + ], + [ + "ecd", + "ECD" + ], + [ + "etd", + "ETD" + ], + [ + "hcd", + "HCD" + ] + ], "msgfplus_style_1": [ [ "cid", @@ -8674,6 +8905,7 @@ "msfragger_style_1": "header_translations", "msfragger_style_2": "header_translations", "msfragger_style_3": "header_translations", + "msfragger_style_4": "header_translations", "msgfplus_style_1": "header_translations", "novor_style_1": "header_translations", "omssa_style_1": "header_translations", @@ -9246,6 +9478,104 @@ "scannum" ] ], + "msfragger_style_4": [ + [ + "charge", + "charge" + ], + [ + "mass_difference", + "massdiff" + ], + [ + "modifications", + "modification_info" + ], + [ + "msfragger:best_locs", + "best_locs" + ], + [ + "msfragger:best_score_with_delta_mass", + "best_score_with_delta_mass" + ], + [ + "msfragger:delta_score", + "delta_score" + ], + [ + "msfragger:expect_score", + "expectscore" + ], + [ + "msfragger:hyperscore", + "hyperscore" + ], + [ + "msfragger:matched_fragment_ions", + "num_matched_ions" + ], + [ + "msfragger:neutral_mass_of_peptide", + "calc_neutral_pep_mass" + ], + [ + "msfragger:next_score", + "nextscore" + ], + [ + "msfragger:number_of_missed_cleavages", + "num_missed_cleavages" + ], + [ + "msfragger:number_of_tryptic_termini", + "num_tol_term" + ], + [ + "msfragger:precursor_neutral_mass_da", + "precursor_neutral_mass" + ], + [ + "msfragger:score_without_delta_mass", + "score_without_delta_mass" + ], + [ + "msfragger:second_best_score_with_delta_mass", + "second_best_score_with_delta_mass" + ], + [ + "msfragger:total_possible_number_of_matched_theoretical_fragment_ions", + "tot_num_ions" + ], + [ + "protein_id", + "protein" + ], + [ + "rank", + "hit_rank" + ], + [ + "retention_time_seconds", + "retention_time" + ], + [ + "sequence", + "peptide" + ], + [ + "sequence_post_aa", + "peptide_next_aa" + ], + [ + "sequence_pre_aa", + "peptide_prev_aa" + ], + [ + "spectrum_id", + "scannum" + ] + ], "msgfplus_style_1": [ [ "calc_mz", @@ -10388,6 +10718,7 @@ "msfragger_style_1": "minimum_ratio", "msfragger_style_2": "minimum_ratio", "msfragger_style_3": "minimum_ratio", + "msfragger_style_4": "minimum_ratio", "omssa_style_1": "-cl", "ptmshepherd_style_1": "spectra_condRatio", "ursgal_style_1": "intensity_cutoff" @@ -10405,6 +10736,7 @@ "description": "Minimum relative intensity (relative to base peak height) for the sum of all diagnostic fragment ion intensities", "key_translations": { "msfragger_style_3": "diagnostic_intensity_filter", + "msfragger_style_4": "diagnostic_intensity_filter", "ursgal_style_1": "intensity_cutoff_diagnostic_ions" }, "name": "intensity_cutoff_diagnostic_ions", @@ -10600,7 +10932,10 @@ "ursgal_style_1": "jobmode" }, "name": "jobmode", - "tag": ["transcriptomics", "cellranger"], + "tag": [ + "transcriptomics", + "cellranger" + ], "triggers_rerun": true, "value_translations": {}, "value_type": "str" @@ -10898,6 +11233,7 @@ "msfragger_style_1": "label", "msfragger_style_2": "label", "msfragger_style_3": "label", + "msfragger_style_4": "label", "msgfplus_style_1": "label", "myrimatch_style_1": "label", "omssa_style_1": [ @@ -10982,6 +11318,7 @@ "msfragger_style_1": "localize_delta_mass", "msfragger_style_2": "localize_delta_mass", "msfragger_style_3": "localize_delta_mass", + "msfragger_style_4": "localize_delta_mass", "ursgal_style_1": "localize_delta_mass" }, "name": "localize_delta_mass", @@ -11021,6 +11358,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] + ], "ursgal_style_1": [ [ false, @@ -11478,6 +11825,7 @@ "msfragger_style_1": "use_topN_peaks", "msfragger_style_2": "use_topN_peaks", "msfragger_style_3": "use_topN_peaks", + "msfragger_style_4": "use_topN_peaks", "myrimatch_style_1": "MaxPeakCount", "ptmshepherd_style_1": "spectra_condPeaks", "ursgal_style_1": "max_accounted_observed_peaks", @@ -11564,6 +11912,7 @@ "msfragger_style_1": "allowed_missed_cleavage", "msfragger_style_2": "allowed_missed_cleavage", "msfragger_style_3": "allowed_missed_cleavage", + "msfragger_style_4": "allowed_missed_cleavage", "msgfplus_style_1": "-maxMissedCleavages", "myrimatch_style_1": "MaxMissedCleavages", "omssa_style_1": "-v", @@ -11721,6 +12070,7 @@ "msfragger_style_1": "max_variable_mods_per_mod", "msfragger_style_2": "max_variable_mods_per_mod", "msfragger_style_3": "max_variable_mods_per_peptide", + "msfragger_style_4": "max_variable_mods_per_peptide", "ursgal_style_1": "max_num_per_mod" }, "name": "max_num_per_mod", @@ -11822,6 +12172,7 @@ "msfragger_style_1": "digest_max_length", "msfragger_style_2": "digest_max_length", "msfragger_style_3": "digest_max_length", + "msfragger_style_4": "digest_max_length", "msgfplus_style_1": "-maxLength", "myrimatch_style_1": "MaxPeptideLength", "omssa_style_1": "-nox", @@ -11845,6 +12196,7 @@ "msfragger_style_1": "max_variable_mods_combinations", "msfragger_style_2": "max_variable_mods_combinations", "msfragger_style_3": "max_variable_mods_combinations", + "msfragger_style_4": "max_variable_mods_combinations", "myrimatch_style_1": "MaxPeptideVariants", "ursgal_style_1": "max_pep_var" }, @@ -12179,6 +12531,7 @@ "msfragger_style_1": "digest_min_length", "msfragger_style_2": "digest_min_length", "msfragger_style_3": "digest_min_length", + "msfragger_style_4": "digest_min_length", "msgfplus_style_1": "-minLength", "myrimatch_style_1": "MinPeptideLength", "omssa_style_1": "-no", @@ -12231,6 +12584,7 @@ "msfragger_style_1": "min_matched_fragments", "msfragger_style_2": "min_matched_fragments", "msfragger_style_3": "min_matched_fragments", + "msfragger_style_4": "min_matched_fragments", "myrimatch_style_1": "MinMatchedFragments", "omssa_style_1": "-hm", "ursgal_style_1": "min_required_matched_peaks", @@ -12250,6 +12604,7 @@ "description": " [labile/glyco search only] Minimum number of sequence-specific (not Y) ions to record a match.", "key_translations": { "msfragger_style_3": "min_sequence_matches", + "msfragger_style_4": "min_sequence_matches", "ursgal_style_1": "min_required_matched_peptide_ions" }, "name": "min_required_matched_peptide_ions", @@ -12266,6 +12621,7 @@ "msfragger_style_1": "minimum_peaks", "msfragger_style_2": "minimum_peaks", "msfragger_style_3": "minimum_peaks", + "msfragger_style_4": "minimum_peaks", "omssa_style_1": "-hs", "ursgal_style_1": "min_required_observed_peaks", "xtandem_style_1": "spectrum, minimum peaks" @@ -12568,6 +12924,7 @@ "msfragger_style_1": "modifications", "msfragger_style_2": "modifications", "msfragger_style_3": "modifications", + "msfragger_style_4": "modifications", "msgfplus_style_1": "-mod", "myrimatch_style_1": [ "DynamicMods", @@ -12622,6 +12979,7 @@ "description": "Specify molecules (or masses) that will be used as mass offsets in the search. Specify as a dictionary with the keys \"chemical_formulas\", \"unimods\", \"glycans\", \"masses\", and lists with the corresponding molecules as values.", "key_translations": { "msfragger_style_3": "mass_offsets", + "msfragger_style_4": "mass_offsets", "ursgal_style_1": "modifications_offsets" }, "name": "modifications_offsets", @@ -12644,6 +13002,7 @@ "description": "Specify molecules (or masses) that will be used as mass offsets for Y-ions in the search. Specify as a dictionary with the keys \"chemical_formulas\", \"unimods\", \"glycans\", \"masses\", and lists with the corresponding molecules as values.", "key_translations": { "msfragger_style_3": "Y_type_masses", + "msfragger_style_4": "Y_type_masses", "ursgal_style_1": "modifications_y_ion_offsets" }, "name": "modifications_y_ion_offsets", @@ -12840,6 +13199,7 @@ "msfragger_style_1": "add_topN_complementary", "msfragger_style_2": "add_topN_complementary", "msfragger_style_3": "add_topN_complementary", + "msfragger_style_4": "add_topN_complementary", "ursgal_style_1": "msfragger_add_topN_complementary" }, "name": "msfragger_add_topN_complementary", @@ -12879,6 +13239,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] + ], "ursgal_style_1": [ [ false, @@ -12897,6 +13267,7 @@ "description": "\"off\" corresponds to a standard MSFragger search, \"labile\" allows to specify delta masses that are searched for, and \"nglycan\" additionally checks for N-glycosylation motifs", "key_translations": { "msfragger_style_3": "labile_search_mode", + "msfragger_style_4": "labile_search_mode", "ursgal_style_1": "msfragger_labile_mode" }, "name": "msfragger_labile_mode", @@ -12914,6 +13285,7 @@ "msfragger_style_1": "min_fragments_modelling", "msfragger_style_2": "min_fragments_modelling", "msfragger_style_3": "min_fragments_modelling", + "msfragger_style_4": "min_fragments_modelling", "ursgal_style_1": "msfragger_min_fragments_modelling" }, "name": "msfragger_min_fragments_modelling", @@ -12932,6 +13304,7 @@ "msfragger_style_1": "output_max_expect", "msfragger_style_2": "output_max_expect", "msfragger_style_3": "output_max_expect", + "msfragger_style_4": "output_max_expect", "ursgal_style_1": "msfragger_output_max_expect" }, "name": "msfragger_output_max_expect", @@ -12950,6 +13323,7 @@ "msfragger_style_1": "track_zero_topN", "msfragger_style_2": "track_zero_topN", "msfragger_style_3": "track_zero_topN", + "msfragger_style_4": "track_zero_topN", "ursgal_style_1": "msfragger_track_zero_topN" }, "name": "msfragger_track_zero_topN", @@ -12968,6 +13342,7 @@ "msfragger_style_1": "zero_bin_accept_expect", "msfragger_style_2": "zero_bin_accept_expect", "msfragger_style_3": "zero_bin_accept_expect", + "msfragger_style_4": "zero_bin_accept_expect", "ursgal_style_1": "msfragger_zero_bin_accept_expect" }, "name": "msfragger_zero_bin_accept_expect", @@ -12985,6 +13360,7 @@ "msfragger_style_1": "zero_bin_mult_expect", "msfragger_style_2": "zero_bin_mult_expect", "msfragger_style_3": "zero_bin_mult_expect", + "msfragger_style_4": "zero_bin_mult_expect", "ursgal_style_1": "msfragger_zero_bin_mult_expect" }, "name": "msfragger_zero_bin_mult_expect", @@ -13762,6 +14138,7 @@ "msfragger_style_1": "output_report_topN", "msfragger_style_2": "output_report_topN", "msfragger_style_3": "output_report_topN", + "msfragger_style_4": "output_report_topN", "msgfplus_style_1": "-n", "myrimatch_style_1": "MaxResultRank", "omssa_style_1": "-hc", @@ -14677,6 +15054,7 @@ "description": " Perform deneutrallossing or not.", "key_translations": { "msfragger_style_3": "deneutralloss", + "msfragger_style_4": "deneutralloss", "ursgal_style_1": "perform_deneutralloss" }, "name": "perform_deneutralloss", @@ -14692,6 +15070,16 @@ true, 1 ] + ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] ] }, "value_type": "bool" @@ -14875,6 +15263,7 @@ "msfragger_style_1": "isotope_error", "msfragger_style_2": "isotope_error", "msfragger_style_3": "isotope_error", + "msfragger_style_4": "isotope_error", "msgfplus_style_1": "-ti", "myrimatch_style_1": "MonoisotopeAdjustmentSet", "omssa_style_1": "-ti", @@ -14987,6 +15376,20 @@ "0/1/2" ] ], + "msfragger_style_4": [ + [ + "0", + "0" + ], + [ + "0,1", + "0/1" + ], + [ + "0,2", + "0/1/2" + ] + ], "myrimatch_style_1": [ [ "0", @@ -15065,6 +15468,7 @@ "description": " One of isolated/selected/recalculated.", "key_translations": { "msfragger_style_3": "precursor_mass_mode", + "msfragger_style_4": "precursor_mass_mode", "ursgal_style_1": "precursor_mass_mode" }, "name": "precursor_mass_mode", @@ -15089,6 +15493,7 @@ "msfragger_style_1": "precursor_mass_lower", "msfragger_style_2": "precursor_mass_lower", "msfragger_style_3": "precursor_mass_lower", + "msfragger_style_4": "precursor_mass_lower", "msgfplus_style_1": "-t_minus", "novor_style_1": "precursorErrorTol_part2", "omssa_style_1": "-te_part1", @@ -15122,6 +15527,7 @@ "msfragger_style_1": "precursor_mass_upper", "msfragger_style_2": "precursor_mass_upper", "msfragger_style_3": "precursor_mass_upper", + "msfragger_style_4": "precursor_mass_upper", "msgfplus_style_1": "-t_plus", "novor_style_1": "precursorErrorTol_part1", "omssa_style_1": "-te_part2", @@ -15149,6 +15555,7 @@ "msfragger_style_1": "precursor_mass_units", "msfragger_style_2": "precursor_mass_units", "msfragger_style_3": "precursor_mass_units", + "msfragger_style_4": "precursor_mass_units", "msgfplus_style_1": "-t_unit", "novor_style_1": "precursorErrorTol_part3", "omssa_style_1": "-teppm", @@ -15224,6 +15631,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + "da", + 0 + ], + [ + "ppm", + 1 + ] + ], "msgfplus_style_1": [ [ "da", @@ -15400,6 +15817,7 @@ "msfragger_style_1": "precursor_max_charge", "msfragger_style_2": "precursor_max_charge", "msfragger_style_3": "precursor_max_charge", + "msfragger_style_4": "precursor_max_charge", "msgfplus_style_1": "-maxCharge", "myrimatch_style_1": "NumChargeStates", "mzml2mgf_style_1": "precursor_max_charge", @@ -15453,6 +15871,7 @@ "msfragger_style_1": "precursor_min_charge", "msfragger_style_2": "precursor_min_charge", "msfragger_style_3": "precursor_min_charge", + "msfragger_style_4": "precursor_min_charge", "msgfplus_style_1": "-minCharge", "mzml2mgf_style_1": "precursor_min_charge", "omssa_style_1": "-zl", @@ -15545,6 +15964,7 @@ "msfragger_style_1": "precursor_true_tolerance", "msfragger_style_2": "precursor_true_tolerance", "msfragger_style_3": "precursor_true_tolerance", + "msfragger_style_4": "precursor_true_tolerance", "ursgal_style_1": "precursor_true_tolerance" }, "name": "precursor_true_tolerance", @@ -15563,6 +15983,7 @@ "msfragger_style_1": "precursor_true_units", "msfragger_style_2": "precursor_true_units", "msfragger_style_3": "precursor_true_units", + "msfragger_style_4": "precursor_true_units", "ursgal_style_1": "precursor_true_units" }, "name": "precursor_true_units", @@ -15602,6 +16023,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + "da", + 0 + ], + [ + "ppm", + 1 + ] + ], "ursgal_style_1": [ [ "da", @@ -15691,7 +16122,8 @@ }, "name": "project", "tag": [ - "transcriptomics", "cellranger" + "transcriptomics", + "cellranger" ], "triggers_rerun": true, "value_translations": {}, @@ -16266,6 +16698,7 @@ "key_translations": { "comet_style_1": "remove_precursor_peak", "msfragger_style_3": "remove_precursor_peak", + "msfragger_style_4": "remove_precursor_peak", "ursgal_style_1": "remove_precursor_peak" }, "name": "remove_precursor_peak", @@ -16306,6 +16739,20 @@ 1 ] ], + "msfragger_style_4": [ + [ + "off", + 0 + ], + [ + "remove_all_charges", + 2 + ], + [ + "remove_precursor_charge", + 1 + ] + ], "ursgal_style_1": [ [ "off", @@ -16336,6 +16783,7 @@ "key_translations": { "mascot_style_1": "CUTOUT", "msfragger_style_3": "remove_precursor_range", + "msfragger_style_4": "remove_precursor_range", "ursgal_style_1": "remove_precursor_range" }, "name": "remove_precursor_range", @@ -16483,6 +16931,7 @@ "description": " If required, PSMs with no precursor peaks will be discarded. For DIA data type only.", "key_translations": { "msfragger_style_3": "require_precursor", + "msfragger_style_4": "require_precursor", "ursgal_style_1": "require_precursor" }, "name": "require_precursor ", @@ -16498,6 +16947,16 @@ true, 1 ] + ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] ] }, "value_type": "bool" @@ -16560,6 +17019,7 @@ "description": " Specify amino acids on which delta masses (mass offsets or search modifications) can occur. Allowed values are single letter codes (e.g. ACD), must be capitalized.", "key_translations": { "msfragger_style_3": "restrict_deltamass_to", + "msfragger_style_4": "restrict_deltamass_to", "ursgal_style_1": "restrict_deltamass_to" }, "name": "restrict_deltamass_to", @@ -16573,6 +17033,7 @@ "description": " Allow the same peak matches to multiple peptides. For DIA data type only.", "key_translations": { "msfragger_style_3": "reuse_dia_fragment_peaks", + "msfragger_style_4": "reuse_dia_fragment_peaks", "ursgal_style_1": "reuse_dia_fragment_peaks" }, "name": "reuse_dia_fragment_peaks ", @@ -16588,6 +17049,16 @@ true, 1 ] + ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] ] }, "value_type": "bool" @@ -16738,7 +17209,10 @@ "ursgal_style_1": "run" }, "name": "run", - "tag": ["transcriptomics", "cellranger"], + "tag": [ + "transcriptomics", + "cellranger" + ], "triggers_rerun": true, "value_translations": {}, "value_type": "str" @@ -16913,7 +17387,10 @@ "ursgal_style_1": "samplesheet" }, "name": "samplesheet", - "tag": ["transcriptomics", "cellranger"], + "tag": [ + "transcriptomics", + "cellranger" + ], "triggers_rerun": true, "value_translations": {}, "value_type": "str" @@ -17056,6 +17533,7 @@ ], "msamanda_style_1": "series", "msfragger_style_3": "fragment_ion_series", + "msfragger_style_4": "fragment_ion_series", "myrimatch_style_1": "FragmentationRule", "omssa_style_1": [ "-i", @@ -18133,6 +18611,7 @@ "mascot_style_1": "unimod_xml_file_list", "msamanda_style_1": "unimod_xml_file_list", "msfragger_style_3": "unimod_xml_file_list", + "msfragger_style_4": "unimod_xml_file_list", "msgfplus_style_1": "unimod_xml_file_list", "novor_style_1": "unimod_xml_file_list", "omssa_style_1": "unimod_xml_file_list", @@ -18222,6 +18701,7 @@ "description": "Use all variable modifications in first search", "key_translations": { "msfragger_style_3": "use_all_mods_in_first_search", + "msfragger_style_4": "use_all_mods_in_first_search", "ursgal_style_1": "use_all_mods_in_first_search" }, "name": "use_all_mods_in_first_search", @@ -18237,6 +18717,16 @@ true, 1 ] + ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] ] }, "value_type": "bool" @@ -18550,6 +19040,7 @@ "msfragger_style_1": "override_charge", "msfragger_style_2": "override_charge", "msfragger_style_3": "override_charge", + "msfragger_style_4": "override_charge", "pepnovo_style_1": "-use_spectrum_charge", "ursgal_style_1": "use_spectrum_charge" }, @@ -18608,6 +19099,16 @@ 0 ] ], + "msfragger_style_4": [ + [ + "no", + 1 + ], + [ + "yes", + 0 + ] + ], "ursgal_style_1": [ [ "no", @@ -21624,6 +22125,7 @@ "description": " Write an MGF with spectra corrected by the calibrated masses ", "key_translations": { "msfragger_style_3": "write_calibrated_mzml", + "msfragger_style_4": "write_calibrated_mzml", "ursgal_style_1": "write_calibrated_mgf" }, "name": "write_calibrated_ms_file", @@ -21642,6 +22144,16 @@ 1 ] ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] + ], "ursgal_style_1": [ [ false, @@ -21660,6 +22172,7 @@ "description": " Put mass difference as a variable modification.", "key_translations": { "msfragger_style_3": "mass_diff_to_variable_mod", + "msfragger_style_4": "mass_diff_to_variable_mod", "ursgal_style_1": "mass_diff_to_variable_mod" }, "name": "write_mass_diff_to_variable_mod", @@ -21675,6 +22188,16 @@ true, 1 ] + ], + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] ] }, "value_type": "bool" @@ -21796,5 +22319,39 @@ ] }, "value_type": "bool" + }, + { + "default_value": false, + "description": "Write uncalibrated MS2 scan to a MZML file. Only for .raw and .d formats.", + "key_translations": { + "ursgal_style_1": "write_uncalibrated_mzml", + "msfragger_style_4": "write_uncalibrated_mzml" + }, + "name": "write_uncalibrated_mzml", + "tag": [], + "triggers_rerun": true, + "value_translations": { + "ursgal_style_1": [ + [ + false, + false + ], + [ + true, + true + ] + ], + "xtandem_style_1": [ + [ + false, + 0 + ], + [ + true, + 1 + ] + ] + }, + "value_type": "bool" } ] \ No newline at end of file diff --git a/jsons/styles.json b/jsons/styles.json index b4af379..01f0128 100644 --- a/jsons/styles.json +++ b/jsons/styles.json @@ -277,6 +277,14 @@ "3.0" ] }, + { + "name": "MSFragger", + "reference": "Kong, A. T., Leprevost, F. V, Avtonomov, D. M., Mellacheruvu, D., and Nesvizhskii, A. I. (2017) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nature Methods 14", + "style": "msfragger_style_4", + "versions": [ + "4.2" + ] + }, { "name": "Merge CSVs", "reference": "Kremer, L. P. M., Leufken, J., Oyunchimeg, P., Schulze, S. & Fufezan, C. (2016) Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis. J. Proteome res. 15, 788-794.", From 070c5773a8c88de31a0538ae13d1bd961926fa83 Mon Sep 17 00:00:00 2001 From: mukul-kandwal Date: Sun, 6 Jul 2025 14:40:17 -0400 Subject: [PATCH 2/5] added to msfragger_style_4 --- jsons/parameters.json | 219 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 216 insertions(+), 3 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index 4c4c7fc..8e01970 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -910,6 +910,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -1112,6 +1120,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -1322,6 +1338,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -1532,6 +1556,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -1742,6 +1774,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -1952,6 +1992,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -2154,6 +2202,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -2356,6 +2412,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -2558,6 +2622,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -2760,6 +2832,14 @@ "msfragger_3_0", true ], + [ + "msfragger_4_1", + true + ], + [ + "msfragger_4_2", + true + ], [ "msgfplus_2021_03_22", false @@ -2954,6 +3034,14 @@ "msfragger_3_0", "msfragger_3_0" ], + [ + "msfragger_4_1", + "msfragger_4_1" + ], + [ + "msfragger_4_2", + "msfragger_4_1" + ], [ "msgfplus_2021_03_22", "msgfplus_2021_03_22" @@ -3735,6 +3823,14 @@ "msfragger_3_0", false ], + [ + "msfragger_4_1", + false + ], + [ + "msfragger_4_2", + false + ], [ "msgfplus_v2016_09_16", true @@ -3945,6 +4041,14 @@ "msfragger_3_0", "msfragger_3_0" ], + [ + "msfragger_4_1", + "msfragger_4_1" + ], + [ + "msfragger_4_2", + "msfragger_4_2" + ], [ "msgfplus_v2016_09_16", "msgfplus_v2016_09_16" @@ -9574,6 +9678,10 @@ [ "spectrum_id", "scannum" + ], + [ + "annotated_delta_mass", + "annotated_delta_mass" ] ], "msgfplus_style_1": [ @@ -15531,8 +15639,8 @@ "msgfplus_style_1": "-t_plus", "novor_style_1": "precursorErrorTol_part1", "omssa_style_1": "-te_part2", - "pyiohat_style_1": " precursor_mass_tolerance_minus", - "pyprotista_style_1": " precursor_mass_tolerance_minus", + "pyiohat_style_1": "precursor_mass_tolerance_plus", + "pyprotista_style_1": "precursor_mass_tolerance_plus", "ursgal_style_1": "precursor_mass_tolerance_plus", "xtandem_style_1": "spectrum, parent monoisotopic mass error plus" }, @@ -15565,6 +15673,7 @@ "pnovo_style_1": "pep_tol_type_ppm", "ptminer_style_1": "precursor_tol_type", "ptmshepherd_style_1": "precursor_mass_units", + "pyiohat_style_1": "precursor_mass_tolerance_unit", "ursgal_style_1": "precursor_mass_tolerance_unit", "xtandem_style_1": "spectrum, parent monoisotopic mass error units" }, @@ -19318,6 +19427,14 @@ "msfragger_3_0", 0 ], + [ + "msfragger_4_1", + 0 + ], + [ + "msfragger_4_2", + 0 + ], [ "msgfplus_v2016_09_16", 1e-100 @@ -19484,6 +19601,14 @@ "msfragger_3_0", "msfragger_3_0" ], + [ + "msfragger_4_1", + "msfragger_4_1" + ], + [ + "msfragger_4_2", + "msfragger_4_2" + ], [ "msgfplus_v2016_09_16", "msgfplus_v2016_09_16" @@ -19694,6 +19819,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -19916,6 +20049,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -20130,6 +20271,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -20352,6 +20501,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -20574,6 +20731,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -20788,6 +20953,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -21002,6 +21175,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -21208,6 +21389,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -21422,6 +21611,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -21636,6 +21833,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -21850,6 +22055,14 @@ "msfragger_3_0", "msfragger:hyperscore" ], + [ + "msfragger_4_1", + "msfragger:hyperscore" + ], + [ + "msfragger_4_2", + "msfragger:hyperscore" + ], [ "msgfplus_2021_03_22", "ms-gf:spec_evalue" @@ -22341,7 +22554,7 @@ true ] ], - "xtandem_style_1": [ + "msfragger_style_4": [ [ false, 0 From 9eaf052046ba1c3c858b0545eb4e1b7357f9422b Mon Sep 17 00:00:00 2001 From: mukul-kandwal Date: Mon, 7 Jul 2025 00:05:49 -0400 Subject: [PATCH 3/5] sorted params.json and styles.json --- jsons/parameters.json | 76 +++++++++++++++++++++---------------------- 1 file changed, 38 insertions(+), 38 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index 8e01970..1edae2b 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -9583,6 +9583,10 @@ ] ], "msfragger_style_4": [ + [ + "annotated_delta_mass", + "annotated_delta_mass" + ], [ "charge", "charge" @@ -9678,10 +9682,6 @@ [ "spectrum_id", "scannum" - ], - [ - "annotated_delta_mass", - "annotated_delta_mass" ] ], "msgfplus_style_1": [ @@ -22451,6 +22451,40 @@ }, "value_type": "str" }, + { + "default_value": false, + "description": "Write uncalibrated MS2 scan to a MZML file. Only for .raw and .d formats.", + "key_translations": { + "msfragger_style_4": "write_uncalibrated_mzml", + "ursgal_style_1": "write_uncalibrated_mzml" + }, + "name": "write_uncalibrated_mzml", + "tag": [], + "triggers_rerun": true, + "value_translations": { + "msfragger_style_4": [ + [ + false, + 0 + ], + [ + true, + 1 + ] + ], + "ursgal_style_1": [ + [ + false, + false + ], + [ + true, + true + ] + ] + }, + "value_type": "bool" + }, { "default_value": false, "description": "Writes rejected results if True", @@ -22532,39 +22566,5 @@ ] }, "value_type": "bool" - }, - { - "default_value": false, - "description": "Write uncalibrated MS2 scan to a MZML file. Only for .raw and .d formats.", - "key_translations": { - "ursgal_style_1": "write_uncalibrated_mzml", - "msfragger_style_4": "write_uncalibrated_mzml" - }, - "name": "write_uncalibrated_mzml", - "tag": [], - "triggers_rerun": true, - "value_translations": { - "ursgal_style_1": [ - [ - false, - false - ], - [ - true, - true - ] - ], - "msfragger_style_4": [ - [ - false, - 0 - ], - [ - true, - 1 - ] - ] - }, - "value_type": "bool" } ] \ No newline at end of file From b6633a4e2c30e3e20c45cfcccfd69c10b29188d2 Mon Sep 17 00:00:00 2001 From: mukul-kandwal Date: Thu, 10 Jul 2025 16:39:42 -0400 Subject: [PATCH 4/5] Added precursor min and max mass params for msfragger 4 open searches --- jsons/parameters.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/jsons/parameters.json b/jsons/parameters.json index 1edae2b..ebf75ec 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -15953,6 +15953,7 @@ "kojak_style_1": "precursor_max_mass", "msfragger_style_1": "precursor_max_mass", "msfragger_style_2": "precursor_max_mass", + "msfragger_style_4": "precursor_mass_upper", "myrimatch_style_1": "MaxPeptideMass", "pglyco_db_style_1": "max_peptide_weight", "pnovo_style_1": "mass_upper_bound", @@ -16005,6 +16006,7 @@ "kojak_style_1": "precursor_min_mass", "msfragger_style_1": "precursor_min_mass", "msfragger_style_2": "precursor_min_mass", + "msfragger_style_4": "precursor_mass_lower", "myrimatch_style_1": "MinPeptideMass", "pglyco_db_style_1": "min_peptide_weight", "pnovo_style_1": "mass_lower_bound", From 14f1445fa5060dfac6aea5a0eca0025eef7d9ebd Mon Sep 17 00:00:00 2001 From: mukul-kandwal Date: Tue, 5 Aug 2025 21:57:40 -0400 Subject: [PATCH 5/5] removed multiple msfragger_style_4 mappings --- jsons/parameters.json | 2 -- 1 file changed, 2 deletions(-) diff --git a/jsons/parameters.json b/jsons/parameters.json index ebf75ec..1edae2b 100644 --- a/jsons/parameters.json +++ b/jsons/parameters.json @@ -15953,7 +15953,6 @@ "kojak_style_1": "precursor_max_mass", "msfragger_style_1": "precursor_max_mass", "msfragger_style_2": "precursor_max_mass", - "msfragger_style_4": "precursor_mass_upper", "myrimatch_style_1": "MaxPeptideMass", "pglyco_db_style_1": "max_peptide_weight", "pnovo_style_1": "mass_upper_bound", @@ -16006,7 +16005,6 @@ "kojak_style_1": "precursor_min_mass", "msfragger_style_1": "precursor_min_mass", "msfragger_style_2": "precursor_min_mass", - "msfragger_style_4": "precursor_mass_lower", "myrimatch_style_1": "MinPeptideMass", "pglyco_db_style_1": "min_peptide_weight", "pnovo_style_1": "mass_lower_bound",