IdentificationParametersCLI
Identification Parameters Command Line Interface
IdentificationParametersCLI can be used to create or edit an identification parameter file via command line, for use in tools like SearchGUI, PeptideMapper 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. Alternatively, the parameters can be created and edited directly in the command lines of CompOmics-utilities, SearchGUI and PeptideShaker.
Note that most of the advanced settings and algorithm specific parameters listed below are for expert usage only. Changes from the default settings should be done with care.
- General command lines
- General parameters
- Spectrum matching parameters
- Advanced parameters
- Algorithm specific parameters
- XTandem advanced parameters
- MS-GF advanced parameters
- MS Amanda advanced parameters
- OMSSA advanced parameters
- MyriMatch advanced parameters
- Comet advanced parameters
- Tide advanced parameters
- Andromeda advanced parameters
- MetaMorpheus advanced parameters
- Sage advanced parameters
- PepNovo advanced parameters
- DirecTag advanced parameters
- pNovo advanced parameters
- Novor advanced parameters
- Comma Separated List
- Help
General command lines
java -cp utilities-X.Y.Z.jar
com.compomics.cli.identification_parameters.IdentificationParametersCLI [parameters]
java -cp SearchGUI-X.Y.Z.jar
eu.isas.searchgui.cmd.IdentificationParametersCLI [parameters]
java -cp PeptideShaker-X.Y.Z.jar
eu.isas.peptideshaker.cmd.IdentificationParametersCLI [parameters]
General parameters
-out The destination Identification Parameters file (.par).
-id_params An identification parameters file to modify (optional).
-mods Lists the available modifications.
-enzymes Lists the available enzymes.
Spectrum matching 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 or 2: Whole Protein. Default is 0.
-enzyme Enzyme, default is 'Trypsin'. Note: case sensitive.
-specificity Specificity of the enzyme:
0: Specific, 1: Semi-Specific, 2: N-term Specific or 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"
-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".
-fixed_mods Fixed modifications as comma separated list,
e.g., "Oxidation of M, Phosphorylation of S"
Note: case sensitive.
-variable_mods Variable modifications as comma separated list,
e.g., "Oxidation of M, Phosphorylation of S"
Note: case sensitive.
-min_charge Minimal charge to search for, default is '2'.
-max_charge Maximal charge to search for, default is '4'.
-fi Type of forward ion searched, default is 'b'.
-ri Type of rewind ion searched, default is 'y'.
-min_isotope Minimum precursor isotope, default is '0'.
-max_isotope Maximum precursor isotope, default is '1'.
Advanced Parameters
The following parameters allow controlling the identification workflow in details. If not set, these settings will be inferred from the Spectrum matching parameters.
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.
percentile: Percentile of the intensities, snp: Signal to noise probability.
Default is percentile.
-annotation_mz_tolerance The m/z tolerance to annotate peaks.
Default: 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. Default is 2.
0: Character Sequence
1: Amino Acids
2: Indistinguishable Amino Acids
-sequence_matching_x The maximal share of Xs in a sequence, 0.25 means 25% of Xs, 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 of missed cleavages to consider when importing identification files,
default is no filter.
-import_missed_cleavages_max
The maximal number of missed cleavages to consider when importing identification files,
default is no filter.
-import_precursor_mz The maximal precursor 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, default is 1.
0: A-score
1: PhosphoRS
2: None
-ptm_threshold The threshold to use for the modification localization 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. Default is 1.
0: Character Sequence
1: Amino Acids
2: Indistinguishable 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.
1: true, 0: false, default is '1'
Note: UniProt databases only.
-updateGeneMapping If true gene mappings will be updated automatically from Ensembl.
1: true, 0: false, default is '1'
Note: UniProt databases only.
Protein Inference
-simplify_groups Simplify protein groups.
1: true, 0: false, default is '1'.
-simplify_evidence Simplify protein groups based on the UniProt protein evidence.
1: true, 0: false, default is '1'.
-simplify_confidence Simplify protein groups based on the peptide confidence.
1: true, 0: false, default is '1'.
-simplify_confidence_threshold
Peptide confidence threshold below which a peptide is considered absent, default is 0.05.
-simplify_enzymaticity Simplify protein groups based on the peptide enzymaticity.
1: true, 0: false, default is '1'.
-simplify_variant Simplify protein groups based on the variant matching
1: true, 0: false, default is '1'.
-pi_modifications Account for modifications when mapping peptides to proteins.
1: true, 0: false, 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'.
Algortithm Specific parameters
The following parameters allow controlling specific identification algorithms specifically.
XTandem 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 '8'.
-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), etd (c, z*)
or manual (a comma-separated list of [abcxyz]
or z* (z+1), e.g. manual:b,y,z).
-myrimatch_termini MyriMatch number of enzymatic termini,
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 peak count 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 '5'.
-ms_amanda_mono MS Amanda use monoisotopic mass values.
0: false, 1: true, default is '1'.
-ms_low_mem_mode MS Amanda use low memory mode option.
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 '8'.
-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: As written in the spectrum or CID if no info,
1: CID, 2: ETD, 3: HCD, 4: UVPD.
Default is '3'.
-msgf_protocol MS-GF+ protocol id option.
0: Automatic (Default)
1: Phosphorylation
2: iTRAQ
3: iTRAQPhospho
4: TMT
5: Standard
-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_matches MS-GF+ maximum number of spectrum matches, default is '10'.
-msgf_additional MS-GF+ additional features.
0: output basic scores only (Default)
1: output additional features
-msgf_termini MS-GF+ number of tolerable termini.
0: non-tryptic
1: semi-tryptic
2: fully-tryptic
Default is '2'.
-msgf_num_ptms MS-GF+ max number of PTMs per peptide, default is '2'.
-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 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 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 '0'.
-omssa_format OMSSA output format.
0: omx, 1: csv, 2: pepXML, default is 'omx'.
Comet advanced parameters
-comet_num_matches Comet maximum number of spectrum matches, default is '10'.
-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_min_peaks Comet min number of peaks for a spectrum, default is '10'.
-comet_min_peak_int Comet min peak intensity, default is '0.0'.
-comet_remove_prec Comet remove precursor peaks:
0: off,
1: all peaks around the precursor m/z,
2: all charge reduced precursor peaks,
3: 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: off
1: 0, +1
2: 0, +1, +2
3: 0, +1, +2, +3
4: -8, -4, 0, +4, +8
Default is '3'.
-comet_min_prec_mass Comet minimum precursor mass, default is '0.0'.
-comet_max_prec_mass Comet maximum precursor mass, default is '10000.0'.
-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 batch size, '0' means load and search all spectra at once,
default is '0'.
-comet_theoretical_fragment_ions
Comet theoretical_fragment_ions option, default is '1'.
-comet_frag_bin_offset Comet fragment bin offset, default is '0.0'.
-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 '8'.
-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_min_ptms Tide min number of PTMs per peptide, 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), 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), default is 'none'.
-tide_keep_terminals Tide keep terminal amino acids when creating decoys (N|C|NC|none), default is 'NC'.
-tide_dedoy_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), 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), default is 'crux-output'.
-tide_verbosity Tide progress display verbosity (0|10|20|30|40|50|60), 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'.
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, Common_Biological, Common_Artifact, Metal, Glyco,
Less_Common, Labeling, Nucleotide_Substitution_One,
Nucleotide_Substitution_TwoPlus, Other.
Sage advanced parameters
-sage_bucket_size Sage bucket size, number of fragments in each
internal mass bucket, default is '32768'.
-sage_min_pep_length Sage minimum peptide length, default is '8'.
-sage_max_pep_length Sage maximum peptide length, default is '30'.
-sage_min_frag_mz Sage minimum fragment mz, default is '200.0'.
-sage_max_frag_mz Sage maximum fragment mz, default is '2000.0'.
-sage_min_pep_mass Sage minimum peptide mass, default is '600.0'.
-sage_max_pep_mass Sage maximum peptide mass, default is '5000.0'.
-sage_min_ion_index Sage minimum ion index for the preliminary search,
default is '2', i.e. skip b1/b2/y1/y2 ions.
-sage_max_var_mods Sage maximum number of variable modifications, default is '2'.
-sage_generate_decoys Sage generate decoys, default is 'true'.
-sage_tmt Sage TMT: Tmt6, Tmt10, Tmt11, Tmt16, or Tmt18.
-sage_tmt_level Sage TMT level: MS-level to perform TMT quantification on, default is '3'.
-sage_tmt_sn Sage use signal/noise instead of intensity for TMT quant, default is 'false'.
-sage_lfq Sage LFQ: default is 'false'.
-sage_lfq_peak_scoring Sage LFQ peak scoring: Hybrid, RetentionTime or SpectralAngle. Default is 'Hybrid'.
-sage_lfq_intergration Sage LFQ integration: Sum or Max. Default is 'Sum'.
-sage_lfq_spectral_angle Sage LFQ spectral angle, default is '0.7'.
-sage_lfq_ppm_tolerance Sage LFQ ppm tolerance, default is '0.5'.
-sage_deisotope Sage deisotope, perform deisotoping and charge state deconvolution,
default is 'false'.
-sage_chimera Sage search for chimeric/co-fragmenting PSMs, default is 'false'.
-sage_wide_window Sage ignore `precursor_tol` and search spectra in wide-window/dynamic
precursor tolerance mode, default is 'false'.
-sage_predict_rt Sage use of retention time prediction model as an feature for LDA,
default is 'true'.
-sage_min_peaks Sage min number of peaks for a spectrum, default is '15'.
-sage_max_peaks Sage max number of peaks for a spectrum, default is '150'.
-sage_min_matched_peaks Sage minimum matched peaks, default is '4'
-sage_max_frag_charge Sage maximum fragment charge, default is 'null'.
-sage_num_psms Sage number of PSMs to report for each spectra.
Recommend setting to 1, higher values might disrupt LDA, default is '1'.
-sage_batch_size Sage batch size, default is the number of CPUs/2.
PepNovo advanced parameters
-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_fragmentation_model
PepNovo+ fragmentation model, default is 'CID_IT_TRYP'.
-pepnovo_generate_blast PepNovo+ generate a BLAST query.
1: true, 0: false, default is '0'.
pNovo advanced parameters
-pnovo_num_peptides pNovo+ number of peptides per spectrum, default is '10'.
-pnovo_lower_prec pNovo+ minimum precursor mass, default is '300'.
-pnovo_upper_prec pNovo+ maximum precursor mass, default is '5000'.
-pnovo_activation pNovo+ actication type (HCD, CID or EDT), default is 'HCD'.
Novor advanced parameters
-novor_fragmentation Novor fragmentation method, CID or HCD, default is 'HCD'.
-novor_mass_analyzer Novor mass analyzer, Trap, TOF, or FT, default is 'FT'.
DirecTag 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'.
Comma Separated List
When using comma separated lists as input for the the PTMs, please pay attention to the quotes required. Surround the full content of the option in quotes and not the individual items:
-variable_mods "Oxidation of M, Phosphorylation of S"
Help
If you experience any problems with the command lines or have any suggestion please contact us via the PeptideShaker mailing list.