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OpenMS
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Peptide Identification with MSFragger
| pot. predecessor tools | → MSFraggerAdapter → | pot. successor tools |
|---|---|---|
| any signal-/preprocessing tool (in mzML format) | IDFilter or any protein/peptide processing tool |
MSFragger must be installed before this adapter can be used. This adapter is fully compatible with version 3.2 of MSFragger and later versions of MSFragger were tested up to version 3.5.
All MSFragger parameters (as specified in the fragger.params file) have been transcribed to parameters of this OpenMS util. It is not possible to provide an explicit fragger.params file to avoid redundancy with the ini file. This adapter creates an fragger.params file prior to calling MSFragger. If the fragger.params file should be inspected, set the -debug option to 2. MSFraggerAdapter will print the path to the working directory to standard out.
MSFragger can process multiple input files (mzML, mzXML) one after another. The number of output files specified must match the number of input spectra files. The output file is then matched to the input file by index. The default parameters of the adapter are the same as given by the official MSFragger manual.
Please cite: Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu & Alexey I Nesvizhskii MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics Nature Methods volume 14, pages 513–520 (2017) doi:10.1038/nmeth.4256
The command line parameters of this tool are:
stty: 'standard input': Inappropriate ioctl for device
MSFraggerAdapter -- Peptide Identification with MSFragger.
Important note:
The Regents of the University of Michigan ("Michigan") grants us permission to redistribute
the MS Fragger application developed by Michigan within the OpenMS Pipeline and make available
for use on related service offerings supported by the University of Tubingen and the Center for
Integrative Bioinformatics.
Per the license agreement the use of the pipeline and associated materials is for academic
research, non-commercial or educational purposes. Any commercial use inquiries
...
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_MSFraggerAdapter.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
+ Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.
To cite MSFraggerAdapter:
+ Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nature Methods volume 14, pages 513–520 (2017). doi:doi:10.1038/nmeth.4256.
Usage:
MSFraggerAdapter <options>
Options (mandatory options marked with '*'):
-license <license>* Set to yes, if you have read and agreed to the MSFragger license terms. (valid: 'yes', 'no')
-java_executable <file> The Java executable. Usually Java is on the system PATH. If Java is not found, use this parameter to specify the full path to Java
-java_heapmemory <num> Maximum Java heap size (in MB) (default: '3500')
-executable <path_to_executable>* Path to the MSFragger executable to use; may be empty if the executable is globally available.
-in <file>* Input File with specta for MSFragger (valid formats: 'mzML', 'mzXML')
-out <file>* MSFragger output file (valid formats: 'idXML')
-opt_out <file> MSFragger optional output file (valid formats: 'pepXML')
-database <path_to_fasta>* Protein FASTA database file path (valid formats: 'FASTA', 'fasta', 'fa', 'fas')
Search Tolerances:
-tolerance:precursor_mass_tolerance_lower <precursor_mass_tolerance> Lower precursor mass tolerance (default: '20.0') (min: '0.0')
-tolerance:precursor_mass_tolerance_upper <precursor_mass_tolerance> Upper precursor mass tolerance (default: '20.0') (min: '0.0')
-tolerance:precursor_mass_unit <precursor_mass_unit> Unit of precursor mass tolerance (default: 'ppm') (valid: 'Da', 'ppm')
-tolerance:precursor_true_tolerance <precursor_true_tolerance> True precursor mass tolerance (window is +/- this value). Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches. (default: '0.0') (min: '0.0')
-tolerance:precursor_true_unit <precursor_true_unit> Unit of precursor true tolerance (default: 'ppm') (valid: 'Da', 'ppm')
-tolerance:fragment_mass_tolerance <fragment_mass_tolerance> Fragment mass tolerance (window is +/- this value) (default: '20.0') (min: '0.0')
-tolerance:fragment_mass_unit <fragment_mass_unit> Unit of fragment mass tolerance (default: 'ppm') (valid: 'Da', 'ppm')
-tolerance:isotope_error <isotope_error> Isotope correction for MS/MS events triggered on isotopic peaks. Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12. (default: '0') (valid: '0', '1', '2', '0/1/2')
In-Silico Digestion Parameters:
-digest:search_enzyme_name <search_enzyme_name> Name of the enzyme to be written to the pepXML file (default: 'Trypsin') (valid: 'Arg-C/P', 'Asp-N', 'Asp-N/B', 'Asp-N_ambic', 'Chymotrypsin', '2-iodobenzoate', 'iodosobenzoate', 'staphylococcal protease/D', 'Trypsin', 'Arg-C', 'Clostripain/P', 'elastase-trypsin-chymotrypsin', 'no cleavage', 'unspecific cleavage', 'Chymotrypsin/P', 'CNBr', 'Formic_acid', 'Lys-C', 'Lys-N', 'Lys-C/P', 'PepsinA', 'TrypChymo', 'Trypsin/P', 'V8-DE', 'V8-E', 'leukocyte elastase', 'proline endopeptidase', 'glutamyl endopeptidase', 'Alpha-lytic protease', 'proline-endopeptidase/HKR', 'Glu-C+P', 'PepsinA + P', 'cyanogen-bromide')
-digest:search_enzyme_cutafter <search_enzyme_cutafter> Residues after which the enzyme cuts (specified as a string of amino acids) (default: 'KR')
-digest:search_enzyme_nocutbefore <search_enzyme_nocutbefore> Residues that the enzyme will not cut before (default: 'P')
-digest:num_enzyme_termini <num_enzyme_termini> Number of enzyme termini (non-enzymatic (0), semi (1), fully (2) (default: 'fully') (valid: 'non-enzymatic', 'semi', 'fully')
-digest:allowed_missed_cleavage <allowed_missed_cleavage> Allowed number of missed cleavages (default: '2') (valid: '0', '1', '2', '3', '4', '5')
-digest:min_length <digest_min_length> Minimum length of peptides to be generated during in-silico digestion (default: '7') (min: '0')
-digest:max_length <digest_max_length> Maximum length of peptides to be generated during in-silico digestion (default: '64') (min: '0')
-digest:mass_range_min <digest_mass_range_min> Min mass of peptides to be generated (Da) (default: '500.0') (min: '0.0')
-digest:mass_range_max <digest_mass_range_max> Max mass of peptides to be generated (Da) (default: '5000.0') (min: '0.0')
Variable Modification Parameters:
-varmod:clip_nterm_m Specifies the trimming of a protein N-terminal methionine as a variable modification
-varmod:masses <varmod1_mass .. varmod7_mass> Masses for variable modifications
-varmod:syntaxes <varmod1_syntax .. varmod7_syntax> Syntax Strings for variable modifications
-varmod:unimod <varmod1_unimod .. varmod7_unimod> Variable modifications in unimod syntax, is added to mass+syntax varmod list
-varmod:enable_common Enable common variable modifications (15.9949 M and 42.0106 [^)
-varmod:not_allow_multiple_variable_mods_on_residue Do not allow any one amino acid to be modified by multiple variable modifications
-varmod:max_variable_mods_per_peptide <max_variable_mods_per_peptide> Maximum total number of variable modifications per peptide (default: '2') (valid: '0', '1', '2', '3', '4', '5')
-varmod:max_variable_mods_combinations <max_variable_mods_combinations> Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534). If a greater number than the maximum is generated, only the unmodified peptide is considered (default: '5000') (min: '0' max: '65534')
Spectrum Processing Parameters:
-spectrum:minimum_peaks <minimum_peaks> Minimum number of peaks in experimental spectrum for matching (default: '10') (min: '0')
-spectrum:use_topn_peaks <use_topN_peaks> Pre-process experimental spectrum to only use top N peaks (default: '50') (min: '0')
-spectrum:minimum_ratio <minimum_ratio> Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity (default: '0.0') (min: '0.0' max: '1.0')
-spectrum:clear_mz_range_min <clear_mz_range_min> Removes peaks in this m/z range prior to matching (minimum value). Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0) (default: '0.0') (min: '0.0')
-spectrum:clear_mz_range_max <clear_mz_range_max> Removes peaks in this m/z range prior to matching (maximum value). Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0) (default: '0.0') (min: '0.0')
-spectrum:max_fragment_charge <max_fragment_charge> Maximum charge state for theoretical fragments to match (default: '2') (valid: '1', '2', '3', '4')
-spectrum:override_charge Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)
-spectrum:precursor_charge_min <precursor_charge_min> Min charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set) (default: '1') (min: '0')
-spectrum:precursor_charge_max <precursor_charge_max> Max charge of precursor charge range to consider. If specified, also spectrum:override_charge must be set) (default: '4') (min: '0')
Open Search Features:
-search:track_zero_topn <track_zero_topn> Track top N unmodified peptide results separately from main results internally for boosting features. Should be set to a number greater than search:output_report_topN if zero bin boosting is desired (default: '0') (min: '0')
-search:zero_bin_accept_expect <zero_bin_accept_expect> Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value (default: '0.0') (min: '0.0')
-search:zero_bin_mult_expect <zero_bin_mult_expect> Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting) (default: '1.0') (min: '0.0')
-search:add_topn_complementary <add_topn_complementary> Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum. Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option (default: '0') (min: '0')
-search:min_fragments_modeling <min_fragments_modeling> Minimum number of matched peaks in PSM for inclusion in statistical modeling (default: '3') (min: '0')
-search:min_matched_fragments <min_matched_fragments> Minimum number of matched peaks for PSM to be reported. MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches (default: '4') (min: '0')
-search:output_report_topn <output_report_topn> Reports top N PSMs per input spectrum (default: '1') (min: '0')
-search:output_max_expect <output_max_expect> Suppresses reporting of PSM if top hit has expectation greater than this threshold (default: '50.0') (min: '0.0')
-search:localize_delta_mass <localize_delta_mass> Include fragment ions mass-shifted by unknown modifications (recommended for open and mass offset searches) (0 for OFF, 1 for ON) (default: '0') (min: '0')
Static Modification Parameters:
-statmod:add_cterm_peptide <add_cterm_peptide> Statically add mass in Da to C-terminal of peptide (default: '0.0') (min: '0.0')
-statmod:add_nterm_peptide <add_nterm_peptide> Statically add mass in Da to N-terminal of peptide (default: '0.0') (min: '0.0')
-statmod:add_cterm_protein <add_cterm_protein> Statically add mass in Da to C-terminal of protein (default: '0.0') (min: '0.0')
-statmod:add_nterm_protein <add_nterm_protein> Statically add mass in Da to N-terminal of protein (default: '0.0') (min: '0.0')
-statmod:unimod <fixedmod1_unimod .. fixedmod7_unimod> Fixed modifications in unimod syntax if specific mass is unknown, e.g. Carbamidomethylation (C). When multiple different masses are given for one aminoacid this parameter (unimod) will have priority.
-reindex <choice> Recalculate peptide to protein association using OpenMS. Annotates target-decoy information. (default: 'true') (valid: 'true', 'false')
PeptideIndexing:
-PeptideIndexing:allow_nterm_protein_cleavage <choice> Allow the protein N-terminus amino acid to clip. (default: 'true') (valid: 'true', 'false')
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
INI file documentation of this tool:
1.9.1