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compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines
http://compomics.github.io/projects/searchgui.html
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Json file format #323

Closed profbiot closed 2 years ago

profbiot commented 2 years ago

SearchGUI on usegalaxy.eu requests a json file that is not described here. What is the format of this "Identification Parameters file"? Can you provide details on what it should contain?

profbiot commented 2 years ago

Here's the text file I got from running the command line command on SearchGUI-4.1.14 installed on a local Linux machine. Is it as simple as converting to json?

============================ IdentificationParametersCLI

IdentificationParametersCLI creates an identification parameters file.

Use the out option to specify the output file or the mods option to list the available modifications.

For further help see https://compomics.github.io/projects/compomics-utilities/wiki/IdentificationParametersCLI.html.

Or contact the developers at https://compomics.github.io/projects/compomics-utilities.html.

OPTIONS

Parameters Files:

-out The destination Identification Parameters file (.par). (Mandatory) -id_params The identification parameters file to use. (Optional)

Search Parameters:

-prec_tol Precursor ion mass tolerance, default is '10'. -prec_ppm Precursor ion tolerance unit: ppm (1) or Da (0), default is '1'. -frag_tol Fragment ion mass tolerance, default is '0.5'. -frag_ppm Fragment ion tolerance unit: ppm (1) or Da (0), default is '1'. -digestion The type of digestion to consider: 0: Enzyme, 1: Unspecific, 2: Whole Protein. Default is 0. -enzyme Enzyme used, default is 'Trypsin'. If more than one enzyme was used, please provide them as comma separated list with quotes, e.g. "Trypsin, Glu-C". See EnzymesCLI to list and edit the enzymes. -specificity Specificity of the enzyme.0: Specific, 1: Semi-Specific, 2: N-term Specific, 3: C-term Specific. If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order as comma separated list with quotes, e.g. "0, 1". -fixed_mods Fixed modifications as comma separated list, e.g., "Oxidation of M, Phosphorylation of S" -variable_mods Variable modifications as comma separated list, e.g., "Oxidation of M, Phosphorylation of S". See ModificationsCLI to list and edit the enzymes -min_charge Minimal charge to search for, default is '2'. -max_charge Maximal charge to search for, default is '4'. -mc Number of allowed missed cleavages, default is '2'. If more than one enzyme was used, please provide the missed cleavages for every enzyme in the same order as comma separated list with quotes, e.g. "2, 1". -fi Type of forward ion searched, default is 'b'. If more than one ion should be used, please provide them as comma separated list with quotes, e.g. "a, b". -ri Type of rewind ion searched, default is 'y'. If more than one ion should be used, please provide them as comma separated list with quotes, e.g. "y, z". -min_isotope Minimal precursor isotope, default is '0'. -max_isotope Maximal precursor isotope, default is '1'.

X!Tandem advanced parameters:

-xtandem_dynamic_range X!Tandem 'spectrum, dynamic range' option, default is '100'. -xtandem_npeaks X!Tandem 'spectrum, total peaks' option, default is '50'. -xtandem_min_frag_mz X!Tandem 'spectrum, minimum fragment mz' option, default is '200'. -xtandem_min_peaks X!Tandem 'spectrum, minimum peaks' option, default is '5'. -xtandem_noise_suppr X!Tandem 'spectrum, use noise suppression' option. 1: true, 0: false, default is '0'. -xtandem_min_prec_mass X!Tandem 'spectrum, minimum parent m+h' option, default is '500'. -xtandem_parent_isotope_correction X!Tandem 'spectrum, parent monoisotopic mass isotope error. 1: true, 0: false, default is '1'. -xtandem_quick_acetyl X!Tandem 'protein, quick acetyl' option. 1: true, 0: false, default is '1'. -xtandem_quick_pyro X!Tandem 'protein, quick pyrolidone' option. 1: true, 0: false, default is '1'. -xtandem_stp_bias X!Tandem 'protein, stP bias' option. 1: true, 0: false, default is '0'. -xtandem_ptm_complexity X!Tandem 'protein, ptm complexity' option, default is '6.0'. -xtandem_refine X!Tandem 'refine' option. 1: true, 0: false, default is '1'. -xtandem_refine_evalue X!Tandem 'refine, maximum valid expectation value' option, default is '0.01'. -xtandem_refine_unc X!Tandem 'refine, unanticipated cleavage' option. 1: true, 0: false, default is '1'. -xtandem_refine_semi X!Tandem 'refine, cleavage semi' option. 1: true, 0: false, default is '0'. -xtandem_refine_pot X!Tandem 'refine, use potential modifications for full refinement' option. 1: true, 0: false, default is '0'. -xtandem_refine_p_mut X!Tandem 'refine, point mutations' option. 1: true, 0: false, default is '0'. -xtandem_refine_snaps X!Tandem 'refine, sNAps' option. 1: true, 0: false, default is '1'. -xtandem_refine_spec_synt X!Tandem 'refine, spectrum synthesis' option. 1: true, 0: false, default is '1'. -xtandem_evalue X!Tandem 'output, maximum valid expectation value' option, default is '0.01'. -xtandem_output_results X!Tandem 'output, results' option (all|valid|stochastic), default is 'all'. -xtandem_output_proteins X!Tandem 'output, proteins' option. 1: true, 0: false, default is '1'. -xtandem_output_sequences X!Tandem 'output, sequences' option. 1: true, 0: false, default is '0'. -xtandem_output_spectra X!Tandem 'output, spectra' option. 1: true, 0: false, default is '1'. -xtandem_output_histograms X!Tandem 'output, histograms' option. 1: true, 0: false, default is '0'. -xtandem_skyline_path X!Tandem 'spectrum, skyline path' option.

MyriMatch advanced parameters:

-myrimatch_min_pep_length MyriMatch minumum peptide length, default is '6'. -myrimatch_max_pep_length MyriMatch maximum peptide length, default is '30'. -myrimatch_min_prec_mass MyriMatch minumum precursor mass, default is '0.0'. -myrimatch_max_prec_mass MyriMatch maximum precursor mass, default is '10000.0'. -myrimatch_num_matches MyriMatch maximum number of spectrum matches, default is '10'. -myrimatch_num_ptms MyriMatch max number of PTMs per peptide, default is '2'. -myrimatch_fragmentation MyriMatch fragmentation method, cid (b, y, true), etd (c, z) or manual (a comma-separated list of [abcxyz] or z (z+1, true), e.g. manual:b,y,z). -myrimatch_termini MyriMatch number of enzymatic termini, e.g. 0: non-tryptic, 1: semi-tryptic, 2: fully-tryptic, default is '2'. -myrimatch_plus_three MyriMatch smart plus three option, 1: true, 0: false, default is '1'. -myrimatch_xcorr MyriMatch xcorr option, 1: true, 0: false, default is '0'. -myrimatch_tic_cutoff MyriMatch TIC cutoff percentage, default is '0.98'. -myrimatch_intensity_classes MyriMatch number of intensity classes, default is '3'. -myrimatch_class_multiplier MyriMatch class multiplier option, default is '2'. -myrimatch_num_batches MyriMatch number of batches option, default is '50'. -myrimatch_max_peak MyriMatch max number of peaks option, default is '100'. -myrimatch_output MyriMatch output format option, mzIdentML or pepXML, default is 'mzIdentML'.

MS Amanda advanced parameters:

-ms_amanda_decoy MS Amanda generate decoys option, 0: false, 1: true, default is '0'. -ms_amanda_decoy_ranking MS Amanda decoys ranking options, 0: shared rank, 1: rank target and decoy separately, default is '1'. -ms_amanda_instrument MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.). -ms_amanda_max_rank MS Amanda maximum rank, default is '10'. -ms_amanda_mono MS Amanda use monoisotopic mass values, 0: false, 1: true, default is '1'. -ms_amanda_perform_deisotoping MS Amanda perform deisotoping, 0: false, 1: true, default is '1'. -ms_amanda_max_mod MS Amanda maximum number of occurrences of a specific modification on a peptide (0-10), default is '3' -ms_amanda_max_var_mod MS Amanda maximum number of variable modifications per peptide (0-10), default is '4' -ms_amanda_max_mod_sites MS Amanda maximum number of potential modification sites per modification per peptide (0-20), default is '6' -ms_amanda_max_neutraul_losses MS Amanda maximum number of water and ammonia losses per peptide (0-5), default is '1' -ms_amanda_max_neutral_losses_mod MS Amanda maximum number identical modification specific losses per peptide (0-5), default is '2' -ms_amanda_min_pep_length MS Amanda minimum peptide length, default is '6' -ms_amanda_max_pep_length MS Amanda maximum peptide length, default is '30' -ms_amanda_loaded_proteins MS Amanda maximum number of proteins loaded into memory (1000-500000), default is '100000' -ms_amanda_loaded_spectra MS Amanda maximum number of spectra loaded into memory (1000-500000), default is '2000' -ms_amanda_output MS Amanda output format option, csv or mzIdentML, default is 'csv'.

MS-GF+ advanced parameters:

-msgf_decoy MS-GF+ search decoys option, 1: true, 0: false, default is '0'. -msgf_instrument MS-GF+ instrument id option, 0: Low-res LCQ/LTQ, 1: Orbitrap/FTICR, 2: TOF, 3: Q-Exactive (Default). -msgf_fragmentation MS-GF+ fragmentation id option, 0: Automatic: as written in the spectrum or CID if no info, 1: CID, 2: ETD, 3: HCD (Default). 4: UVPD. -msgf_protocol MS-GF+ protocol id option, 0: Automatic (Default, true), 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho, 4: TMT, 5: Standard. -msgf_termini MS-GF+ number of tolerable termini, e.g. 0: Non required, 1: At least one, 2: Both, default is '2'. -msgf_min_pep_length MS-GF+ minumum peptide length, default is '8'. -msgf_max_pep_length MS-GF+ maximum peptide length, default is '30'. -msgf_num_ptms MS-GF+ max number of PTMs per peptide, default is '2'. -msgf_num_matches MS-GF+ maximum number of spectrum matches, default is '10'. -msgf_additional MS-GF+ additional output, 0: output basic scores only (Default, true), 1: output additional features. -msgf_num_tasks MS-GF+ number of tasks as an integer, default: internally calculated based on inputs

OMSSA advanced parameters:

-omssa_low_intensity OMSSA low intensity cutoff as percentage of the most intense peak, default is '0.0'. -omssa_high_intensity OMSSA high intensity cutoff as percentage of the most intense peak, default is '0.2'. -omssa_intensity_incr OMSSA intensity cutoff increment, default is '0.0005'. -omssa_min_peaks OMSSA minimum number of peaks, integer, default is '4'. -omssa_remove_prec OMSSA eliminate charge reduced precursors in spectra option, 1: true, 0: false, default is '0'. -omssa_estimate_charge OMSSA estimate precursor charge option, 1: Use range, 0: Believe input file, default is '1'. -omssa_plus_one OMSSA estimate plus one charge algorithmically option, 1: true, 0: false, default is '1'. -omssa_fraction OMSSA fraction of precursor m/z for charge charge one estimation, default is '0.95'. -omssa_prec_per_spectrum OMSSA minimum number of precursors per spectrum, integer, default is '1'. -omssa_scale_prec OMSSA scale precursor mass option, 1: true, 0: false, default is '1'. -omssa_memory OMSSA map sequences in memory option, 1: true, 0: false, default is '1'. -omssa_methionine OMSSA N-terminal methionine cleavage option, 1: true, 0: false, default is '1'. -omssa_neutron Mass after which OMSSA should consider neutron exact mass, default is '1446.94'. -omssa_single_window_wd OMSSA single charge window width in Da, integer, default is '27'. -omssa_double_window_wd OMSSA double charge window width in Da, integer, default is '14'. -omssa_single_window_pk OMSSA single charge window number of peaks, integer, default is '2'. -omssa_double_window_pk OMSSA double charge window number of peaks, integer, default is '2'. -omssa_min_ann_int_pks OMSSA minimum number of annotated peaks among the most intense ones, integer, default is '6'. -omssa_min_annotated_peaks OMSSA minimum number of annotated peaks, integer, default is '2'. -omssa_max_ladders OMSSA maximum number of m/z ladders, integer, default is '128'. -omssa_max_frag_charge OMSSA maximum fragment charge, integer, default is '2'. -omssa_charge OMSSA fragment charge option, 1: plus, 0: minus, default is '1'. -omssa_forward OMSSA include first forward ion (b1) in search, 1: true, 0: false, default is '0'. -omssa_rewind OMSSA search rewind (C-terminal) ions option, 1: true, 0: false, default is '1'. -omssa_max_frag_series OMSSA maximum fragment per series option, integer, default is '100'. -omssa_corr OMSSA use correlation correction score option, 1: true, 0: false, default is '1'. -omssa_consecutive_p OMSSA consecutive ion probability, default is '0.5'. -omssa_hitlist_charge OMSSA number of hits per spectrum per charge, default is '30'. -omssa_it_sequence_evalue OMSSA e-value cutoff to consider a sequence in the iterative search 0.0 means all, default is '0.0'. -omssa_it_spectrum_evalue OMSSA e-value cutoff to consider a spectrum in the iterative search 0.0 means all, default is '0.01'. -omssa_it_replace_evalue OMSSA e-value cutoff to replace a hit in the iterative search 0.0 means keep best, default is '0.0'. -omssa_min_pep_length OMSSA minumum peptide length (semi-tryptic or no enzyme searches only). -omssa_max_pep_length OMSSA maximum peptide length (OMSSA semi-tryptic or no enzyme searches only). -omssa_max_evalue OMSSA maximal evalue considered, default is '100'. -omssa_hitlist_length OMSSA hitlist length, 0 means all, default is '10'. -omssa_format OMSSA output format. 0: omx, 1: csv, 2: pepXML, default is 'omx'.

Comet advanced parameters:

-comet_min_peaks Comet min number of peaks for a spectrum, default is '10'. -comet_min_peak_int Comet minimal peak intensity, default is '0.0'. -comet_remove_prec Comet remove precursor peaks, 0: no, 1: yes, 2: yes + all charge reduced precursor peaks, 3: yes + precursor phosphate neutral loss peaks, default is '0'. -comet_remove_prec_tol Comet remove precursor tolerance, default is '1.5'. -comet_clear_mz_range_lower Comet clear mz range lower, default is '0.0'. -comet_clear_mz_range_upper Comet clear mz range upper, default is '0.0'. -comet_enzyme_type Comet enzyme type, 1: semi-specific, 2: full-enzyme, 8: unspecific N-term, 9: unspecific C-term, default is '2'. -comet_isotope_correction Comet isotope correction, 0: no correction, 1: 0, +1, 2: 0, +1, +2, 3: 0,+1,+2,+3, 4: -8,-4,0,+4,+8, default is '1'. -comet_min_prec_mass Comet minimum precursor mass, default is '600.0'. -comet_max_prec_mass Comet maximum precursor mass, default is '5000.0'. -comet_min_pep_length Comet minimum peptide length, default is '8'. -comet_max_pep_length Comet maximum peptide length, default is '30'. -comet_max_frag_charge Comet maximum fragment charge [1-5], default is '3'. -comet_remove_meth Comet remove methionine, 1: true, 0: false, default is '0'. -comet_batch_size Comet spectrum batch size, '0' means load and search all spectra at once, default is '0'. -comet_num_ptms Comet max number of variable PTMs per peptide, default is '10'. -comet_req_ptms Comet require at least one variable PTM per peptide, 1: true, 0: false, default is '0'. -comet_theoretical_fragment_ions Comet theoretical_fragment_ions option, it is the correlation score type, 1: true, 0: false, default is '1'. -comet_frag_bin_offset Comet fragment bin offset, default is '0.01'. -comet_num_matches Comet maximum number of spectrum matches, default is '10'. -comet_output Comet output type, PepXML, SQT, TXT, Percolator or mzIdentML, default is 'PepXML'.

Tide advanced parameters:

-tide_min_pep_length Tide minumum peptide length, default is '6'. -tide_max_pep_length Tide maximum peptide length, default is '30'. -tide_min_prec_mass Tide minumum precursor mass, default is '200.0'. -tide_max_prec_mass Tide maximum precursor mass, default is '7200.0'. -tide_monoisotopic Tide monoisotopic precursor, 1: true, 0: false, default is '1'. -tide_clip_n_term Tide clip n term methionine, 1: true, 0: false, default is '0'. -tide_max_ptms Tide max number of PTMs per peptide, default is '255'. -tide_num_ptms_per_type Tide max number of PTMs of each type per peptide, default is '2'. -tide_digestion_type Tide digetion type (full-digest or partial-digest, true), default is 'full-digest'. -tide_print_peptides Tide print peptides, 1: true, 0: false, default is '0'. -tide_decoy_format Tide decoy fomat (none|shuffle|peptide-reverse|protein-reverse, true), default is 'none'. -tide_keep_terminals Tide keep terminal amino acids when creating decoys (N|C|NC|none, true), default is 'NC'. -tide_decoy_seed Tide decoy seed, default is '1'. -tide_remove_temp Tide remove temp folders when the search is done, 1: true, 0: false, default is '1'. -tide_compute_p Tide compute exact p-values, 1: true, 0: false, default is '0'. -tide_compute_sp Tide compute sp score, 1: true, 0: false, default is '0'. -tide_min_spectrum_mz Tide minimum spectrum mz, default is '0.0'. -tide_max_spectrum_mz Tide maximum spectrum mz, default is no limit. -tide_min_spectrum_peaks Tide min spectrum peaks, default is '20'. -tide_spectrum_charges Tide spectrum charges (1|2|3|all, true), default is 'all'. -tide_remove_prec Tide remove precursor, 1: true, 0: false, default is '0'. -tide_remove_prec_tol Tide remove precursor tolerance, default is '1.5'. -tide_use_flanking Tide use flanking peaks, 1: true, 0: false, default is '0'. -tide_use_neutral_losses Tide use neutral losses peaks, 1: true, 0: false, default is '0'. -tide_mz_bin_width Tide mz bin width, default is '0.02'. -tide_mz_bin_offset Tide mz bin offset, default is '0.0'. -tide_max_psms Tide maximum number of spectrum matches spectrum, default is '10'. -tide_export_text Tide export text file, 1: true, 0: false, default is '1'. -tide_export_sqt Tide export SQT file, 1: true, 0: false, default is '0'. -tide_export_pepxml Tide export pepxml, 1: true, 0: false, default is '0'. -tide_export_mzid Tide export mzid, 1: true, 0: false, default is '0'. -tide_export_pin Tide export Percolator input file, 1: true, 0: false, default is '0'. -tide_output_folder Tide output folder (relative to the Tide working folder, true), default is 'crux-output'. -tide_verbosity Tide progress display verbosity (0|10|20|30|40|50|60, true), default is '30'. -tide_progress_indicator Tide progress indicator frequency, default is '1000'. -tide_concat Tide concatenate target and decoy results, 1: true, 0: false, default is '0'. -tide_store_spectra Tide file name in with to store the binary spectra, default is null, i.e., not set.

Andromeda advanced parameters:

-andromeda_max_pep_mass Andromeda maximum peptide mass, default is '4600.0'. -andromeda_max_comb Andromeda maximum combinations, default is '250'. -andromeda_top_peaks Andromeda number of top peaks, default is '8'. -andromeda_top_peaks_window Andromeda top peaks window width, default is '100'. -andromeda_incl_water Andromeda account for water losses, 1: true, 0: false, default is '1'. -andromeda_incl_ammonia Andromeda account for ammonina losses, 1: true, 0: false, default is '1'. -andromeda_neutral_losses Andromeda neutral losses are sequence dependent, 1: true, 0: false, default is '1'. -andromeda_fragment_all Andromeda fragment all option, 1: true, 0: false, default is '0'. -andromeda_emp_correction Andromeda emperical correction, 1: true, 0: false, default is '1'. -andromeda_higher_charge Andromeda higher charge option, 1: true, 0: false, default is '1'. -andromeda_frag_method Andromeda fragmentation method, HCD, CID or EDT, default is 'CID'. -andromeda_max_mods Andromeda maximum number of modifications, default is '5'. -andromeda_min_pep_length Andromeda minimum peptide length when using no enzyme, default is '8'. -andromeda_max_pep_length Andromeda maximum peptide length when using no enzyme, default is '30'. -andromeda_equal_il Andromeda whether I and L should be considered indistinguishable, 1: true, 0: false, default is '0'. -andromeda_max_psms Andromeda maximum number of spectrum matches spectrum, default is '10'. -andromeda_decoy_mode Andromeda decoy mode, none or decoy, default is 'none'.

MetaMorpheus advanced parameters:

-meta_morpheus_min_pep_length MetaMorpheus minimum peptide length, default is '8'. -meta_morpheus_max_pep_length MetaMorpheus maximum peptide length, default is '30'. -meta_morpheus_search_type MetaMorpheus search type, Classic, Modern or NonSpecific, default is 'Classic'. -meta_morpheus_num_partitions MetaMorpheus number of partitions when indexing, default is '1'. -meta_morpheus_dissociation_type MetaMorpheus dissociation type, HCD, CID, ECD or ETD, default is 'HCD'. -meta_morpheus_max_mods_for_peptide MetaMorpheus maximum modifications per peptide, default is '2'. -meta_morpheus_meth MetaMorpheus initiator methionine behavior, Undefined, Retain, Cleave or Variable, default is 'Variable'. -meta_morpheus_score_cutoff MetaMorpheus score cutoff, default is '5.0'. -meta_morpheus_use_delta_score MetaMorpheus use delta score, 1: true, 0: false, default is '0'. -meta_morpheus_frag_term MetaMorpheus fragmentation terminus, Both, N or C, default is 'Both'. -meta_morpheus_max_frag_size MetaMorpheus maximum fragmentation size, default is '30000'. -meta_morpheus_min_internal_fragment_length MetaMorpheus minimum allowed internal fragment length, default is '0'. -meta_morpheus_mass_diff_acceptor_type MetaMorpheus mass difference acceptor type, Exact, OneMM, TwoMM, ThreeMM, PlusOrMinusThreeMM, ModOpen or Open, default is 'OneMM'. -meta_morpheus_write_mzid MetaMorpheus write mzid, 1: true, 0: false, default is '1'. -meta_morpheus_write_pepxml MetaMorpheus write pepxml, 1: true, 0: false, default is '0'. -meta_morpheus_use_provided_prec MetaMorpheus use provided precursor info, 1: true, 0: false, default is '1'. -meta_morpheus_do_prec_deconv MetaMorpheus do precursor deconvolution, 1: true, 0: false, default is '1'. -meta_morpheus_deconv_int_ratio MetaMorpheus deconvolution intensity ratio, default is '3.0'. -meta_morpheus_deconv_mass_tol MetaMorpheus deoconvolution mass tolerance, default is '4.0'. -meta_morpheus_deconv_mass_tol_type MetaMorpheus deoconvolution mass tolerance type, PPM or Absolute, default is 'PPM'. -meta_morpheus_trim_ms1 MetaMorpheus trim MS1 peaks, 1: true, 0: false, default is '0'. -meta_morpheus_trim_msms MetaMorpheus trim MSMS peaks, 1: true, 0: false, default is '1'. -meta_morpheus_num_peaks_per_window MetaMorpheus number of peaks per window, default is '200'. -meta_morpheus_min_allowed_int_ratio_to_base_peak MetaMorpheus minium allowed intensity ratio to base peak, default is '0.01'. -meta_morpheus_window_with_thompson MetaMorpheus window width in Thompson. -meta_morpheus_num_windows MetaMorpheus number of windows. -meta_morpheus_norm_across_all_windows MetaMorpheus normalize peaks across all windows, 1: true, 0: false, default is '0'. -meta_morpheus_mod_peptides_are_different MetaMorpheus modified peptides are different, 1: true, 0: false, default is '0'. -meta_morpheus_no_one_hit_wonders MetaMorpheus exclude one hit wonders, 1: true, 0: false, default is '0'. -meta_morpheus_search_target MetaMorpheus search target sequences, 1: true, 0: false, default is '1'. -meta_morpheus_decoy_type MetaMorpheus decoy type, None, Reverse or Slide, default is 'None'. -meta_morpheus_max_mod_isoforms MetaMorpheus maximum modified isoforms, default is '1024'. -meta_morpheus_min_variant_depth MetaMorpheus minimum variant depth, default is '1'. -meta_morpheus_max_hetrozygous_var MetaMorpheus maximum hetrozygous variants, default is '4'. -meta_morpheus_gptm MetaMorpheus run G-PTM, 1: true, 0: false, default is '0'. -meta_morpheus_gptm_categories MetaMorpheus G-PTM categories to include in the G-PTM search: Common Fixed and Variable, Common Biological, Common Artifact, Metal, Glycosylation, Less Common, Labeling, Substitution (1 Nucleotide), Substitution (2+ Nucleotides), Other.

Novor:

-novor_fragmentation Novor fragmentation method, CID or HCD, default is 'HCD'. -novor_mass_analyzer Novor mass analyzer, Trap, TOF, or FT, default is 'FT'.

PNovo+:

-pnovo_activation pNovo+ activation type (HCD, CID or EDT, true), default is 'HCD'. -pnovo_lower_prec pNovo+ minimum precursor mass, default is '300'. -pnovo_upper_prec pNovo+ maximum precursor mass, default is '5000'. -pnovo_num_peptides pNovo+ number of peptides per spectrum, default is '10'.

PepNovo+:

-pepnovo_hitlist_length PepNovo+ number of de novo solutions [0-2000], default is '10'. -pepnovo_estimate_charge PepNovo+ estimate precursor charge option. 1: true, 0: false, default is '1'. -pepnovo_correct_prec_mass PepNovo+ correct precursor mass option. 1: true, 0: false, default is '1'. -pepnovo_discard_spectra PepNovo+ discard low quality spectra optoin. 1: true, 0: false, default is '1'. -pepnovo_generate_blast PepNovo+ generate a BLAST query. 1: true, 0: false, default is '0'.

DirectTag advanced parameters:

-directag_tag_length DirecTag tag length, default is '4'. -directag_max_var_mods DirecTag maximum variable modifications per sequence, default is '2'. -directag_charge_states DirecTag number of charge states considered, default is '3'. -directag_duplicate_spectra DirecTag duplicate spectra per charge, 1: true, 0: false, default is '1'. -directag_isotope_tolerance DirecTag isotope mz tolerance, default is '0.25'. -directag_deisotoping DirecTag deisotoping mode, default is '0', 0: no deisotoping, 1: precursor only, 2: precursor and candidate. -directag_intensity_classes DirecTag number of intensity classses, default is '3'. -directag_output_suffix DirecTag output suffic, default is no suffix. -directag_max_peak_count DirecTag max peak count, default is '100'. -directag_max_tag_count DirecTag maximum tag count, default is '10'. -directag_tic_cutoff DirecTag TIC cutoff in percent, default is '100'. -directag_complement_tolerance DirecTag complement mz tolerance, default is '0.1'. -directag_adjustment_step DirecTag precursor adjustment step, default is '0.1'. -directag_min_adjustment DirecTag minimum precursor adjustment, default is '-0.5'. -directag_max_adjustment DirecTag maximum precursor adjustment, default is '1.5'. -directag_intensity_weight DirecTag intensity score weight, default is '1.0'. -directag_fidelity_weight DirecTag fidelity score weight, default is '1.0'. -directag_complement_weight DirecTag complement_score_weight, default is '1.0'. -directag_adjust_precursor DirecTag adjust precursor, 1: true, 0: false, default is '0'. -directag_ms_charge_state DirecTag use charge state from M spectrum, 1: true, 0: false, default is '1'.

Spectrum Annotation:

-annotation_level The intensity threshold to consider for annotation, e.g. using percentiles, 0.75 means that the 25% most intense peaks will be annotated, default is 0.75. -annotation_level_type The type of the intensity threshold. (valid values: percentile: Percentile of the intensities, snp: Signal to noise probability, default is percentile). -annotation_mz_tolerance The m/z tolerance to annotate peaks, default is equal to the search settings MS2 tolerance. -annotation_high_resolution If true the most accurate peak will be selected within the m/z tolerance. (1: true, 0: false, default is '1')

Sequence Matching:

-sequence_matching_type The peptide to protein sequence matching type. (0: Character Sequence, 1: Amino Acids, 2: Indistinguishable Amino Acids, default is Indistinguishable Amino Acids) -sequence_matching_x The maximum share of X's in a sequence, 0.25 means 25% of X's, default is 0.25. -sequence_matching_enzymatic_tags Tags should only be mapped to enzymatic peptides. (1: true, 0: false, default is '0') -sequence_matching_max_ptms_per_tag The maximum number of PTMs per peptide when mapping tags, default is 3. -sequence_matching_min_amino_acid_score The minimum amino acid score when mapping tags, default is 30. -sequence_matching_min_tag_length The minimum tag length when mapping tags, default is 3.

Import Filters:

-import_peptide_length_min The minimal peptide length to consider when importing identification files, default is 8. -import_peptide_length_max The maximal peptide length to consider when importing identification files, default is 30. -import_missed_cleavages_min The minimal number if missed cleavages to consider when importing identification files, default is no filter. -import_missed_cleavages_max The maximal number if missed cleavages to consider when importing identification files, default is no filter. -import_precursor_mz The maximal precursor deviation to allow when importing identification files, the precursor tolerance by default. -import_precursor_mz_ppm Maximal precursor ion deviation unit: ppm (1) or Da (0), default is '1'. -exclude_unknown_ptms If true peptides presenting unrecognized PTMs will be excluded. (1: true, 0: false, default is '1')

PTM Localization:

-ptm_score The PTM probabilistic score to use for modification localization (1: PhosphoRS,2: None, default is '1'). -ptm_threshold The threshold to use for the modification localizatoin score. Default is 95. -score_neutral_losses Include neutral losses in spectrum annotation of the PTM score (1: true, 0: false, default is '0'). -ptm_sequence_matching_type The modification to peptide sequence matching type. (0: Character Sequence, 1: Amino Acids, 2: Indistinguishable Amino Acids, default is Amino Acids) -ptm_alignment Align peptide ambiguously localized PTMs on confident sites (1: true, 0: false, default is '1').

Gene Annotation:

-useGeneMapping If true gene mappings will be used and saved along with the project (UniProt databases only). (1: true, 0: false, default is '1') -updateGeneMapping If true gene mappings will be updated automatically from Ensembl (UniProt databases only). (1: true, 0: false, default is '1')

Protein Inference:

-simplify_groups Simplify protein groups, 1: yes, 0: no, default is 1. -simplify_enzymaticity Simplify protein groups based on the peptide enzymaticity, 1: yes, 0: no, default is 1. -simplify_evidence Simplify protein groups based on the Uniprot protein evidence, 1: yes, 0: no, default is 1. -simplify_confidence Simplify protein groups based on the peptide confidence, 1: yes, 0: no, default is 1. -simplify_confidence_threshold Peptide confidence threshold below which a peptide is considered absent, default is 0.05. -simplify_variant Simplify protein groups based on the variant matching, 1: yes, 0: no, default is 1. -pi_modifications Account for modifications when mapping peptides to proteins, 1: yes, 0: no, default is 1.

Validation Levels:

-psm_fdr FDR at the PSM level in percent, default is 1. -peptide_fdr FDR at the peptide level in percent, default is 1. -protein_fdr FDR at the protein level in percent, default is 1.

Fraction Analysis:

-protein_fraction_mw_confidence Minimum confidence required for a protein in the fraction MW plot (default 95%: '95.0').

Database Processing:

-fasta_target_decoy FASTA file should be processed as target-decoy. 1: true, 0: false, default is '1'. -fasta_decoy_tag The flag for decoy proteins in the accession. Default is '-REVERSED'. -fasta_decoy_type Decoy type. 0: prefix, 1: suffix, default is '1'. -fasta_decoy_file_tag The tag added after adding decoy sequences to a FASTA file. Default is '_concatenated_target_decoy'.

Help:

-mods Lists the available modifications. -usage Lists the available options.

hbarsnes commented 2 years ago

The json parameter file can be created using the Identification Parameters tool at usegalaxy.eu. We recommend setting up a workflow where the output from the Identification Parameters tool is used as input to SearchGUI.

If you want to create the parameter file externally via the command line you can do this via https://github.com/compomics/compomics-utilities/wiki/IdentificationParametersCLI.