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Searchgui searchcli6/20/2023 myrimatch_max_peak MyriMatch max peak count option, default is '100'. myrimatch_num_batches MyriMatch number of batches option, default is '50'. MyriMatch class multiplier option, default is '2'. MyriMatch number of intensity classes, default is '3'. myrimatch_tic_cutoff MyriMatch TIC cutoff percentage, default is '0.98'. myrimatch_plus_three MyriMatch smart plus three option, myrimatch_termini MyriMatch number of enzymatic termini, myrimatch_fragmentation MyriMatch fragmentation method, myrimatch_num_ptms MyriMatch max number of PTMs per peptide, default is '2'. myrimatch_num_matches MyriMatch maximum number of spectrum matches, default is '10'. myrimatch_max_prec_mass MyriMatch maximum precursor mass, default is '10000.0'. myrimatch_min_prec_mass MyriMatch minumum precursor mass, default is '0.0'. myrimatch_max_pep_length MyriMatch maximum peptide length, default is '30'. myrimatch_min_pep_length MyriMatch minumum peptide length, default is '8'. xtandem_skyline_path X!Tandem 'spectrum, skyline path' option. xtandem_output_spectra X!Tandem 'output, spectra' option. xtandem_output_sequences X!Tandem 'output, sequences' option. xtandem_output_proteins X!Tandem 'output, proteins' option. xtandem_output_results X!Tandem 'output, results' option (all|valid|stochastic), default is 'all'. xtandem_evalue X!Tandem 'output, maximum valid expectation value' option, default is '0.01'. xtandem_refine_spec_synt X!Tandem 'refine, spectrum synthesis' option. xtandem_refine_snaps X!Tandem 'refine, sNAps' option. xtandem_refine_p_mut X!Tandem 'refine, point mutations' option. xtandem_refine_pot X!Tandem 'refine, use potential modifications for full refinement' option. xtandem_refine_semi X!Tandem 'refine, cleavage semi' option. xtandem_refine_unc X!Tandem 'refine, unanticipated cleavage' option. xtandem_refine_evalue X!Tandem 'refine, maximum valid expectation value' option, default is '0.01'. xtandem_refine X!Tandem 'refine' option. xtandem_ptm_complexity X!Tandem 'protein, ptm complexity' option, default is '6.0'. xtandem_stp_bias X!Tandem 'protein, stP bias' option. xtandem_quick_pyro X!Tandem 'protein, quick pyrolidone' option. xtandem_quick_acetyl X!Tandem 'protein, quick acetyl' option. X!Tandem 'spectrum, parent monoisotopic mass isotope error. xtandem_min_prec_mass X!Tandem 'spectrum, minimum parent m+h' option, default is '500'. xtandem_noise_suppr X!Tandem 'spectrum, use noise suppression' option. xtandem_min_peaks X!Tandem 'spectrum, minimum peaks' option, default is '5'. xtandem_min_frag_mz X!Tandem 'spectrum, minimum fragment mz' option, default is '200'. xtandem_npeaks X!Tandem 'spectrum, total peaks' option, default is '50'. xtandem_dynamic_range X!Tandem 'spectrum, dynamic range' option, default is '100'. If not set, these settings will be inferred from the Spectrum matching parameters. The following parameters allow controlling the identification workflow in details. max_isotope Maximum precursor isotope, default is '1'. min_isotope Minimum precursor isotope, default is '0'. ri Type of rewind ion searched, default is 'y'. fi Type of forward ion searched, default is 'b'. max_charge Maximal charge to search for, default is '4'. min_charge Minimal charge to search for, default is '2'. variable_mods Variable modifications as comma separated list, fixed_mods Fixed modifications as comma separated list,Į.g., "Oxidation of M, Phosphorylation of S" If more than one enzyme was used, please provide the missed cleavages for everyĮnzyme in the same order as comma separated list with quotes, e.g. mc Number of allowed missed cleavages, default is '2'. If more than one enzyme was used, please provide the missed cleavages forĮvery enzyme in the same order as comma separated list with quotes, e.g. Note: case sensitive.Ġ: Specific, 1: Semi-Specific, 2: N-term Specific or 3: C-term Specific digestion The type of digestion to consider:Ġ: Enzyme, 1: Unspecific or 2: Whole Protein. frag_ppm Fragment ion tolerance unit: ppm (1) or Da (0), default is '1'. frag_tol Fragment ion mass tolerance, default is '0.5'. prec_ppm Precursor ion tolerance unit: ppm (1) or Da (0), default is '1'. prec_tol Precursor ion mass tolerance, default is '10'. Changes from the default settings should be done with care. Note that most of the advanced settings and algorithm specific parameters listed below are for expert usage only. Alternatively, the parameters can be created and edited directly in the command lines of CompOmics-utilities, SearchGUI and PeptideShaker. Identification parameter files are in the json format and can also be created in the graphical user interface or using third party tools. IdentificationParametersCLI can be used to create or edit an identification parameter file via command line, for use in tools like SearchGUI, PeptideMapper and PeptideShaker. IdentificationParametersCLI Identification Parameters Command Line Interface
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