OpenMS
2.4.0
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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.
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:
MSFraggerAdapter -- Peptide Identification with MSFragger Version: 2.4.0 Oct 29 2018, 15:52:19, Revision: 9690d06 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. 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 '*'): -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 execut able is globally available. -in <file>* Input File with specta for MSFragg er (valid formats: 'mzML', 'mzXML' ) -out <file>* MSFragger output file (valid forma ts: '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 <precursor_mass_tolerance> Precursor mass tolerance (window is +/- this value) (default: '20' min: '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 (win dow is +/- this value). Used for tie breaker of results (in spectra lly ambiguous cases) and zero bin boosting in open searches (0 disab les these features). This option is STRONGLY recommended for open searches. (default: '0' min: '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' min: '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 event s triggered on isotopic peaks. Should be set to 0 (disabled) for open search or 0/1/2 for correctio n of narrow window searches. Shift s the precursor mass window to multiples of this value multiplied by the mass of C13-C12. (default: '0' valid: '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: 'Tryp sin' valid: 'Arg-C/P', 'Trypsin', 'Arg-C', 'Asp-N/B', 'Chymotrypsin' , 'Chymotrypsin/P', 'CNBr', 'Formi c_acid', 'Lys-C', 'Lys-N', 'Lys-C/ P', 'PepsinA', 'TrypChymo', 'Tryps in/P', 'V8-DE', 'V8-E', 'leukocyte ... cleavage', 'Asp-N', 'Asp-N_ambic') -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-enzy matic (0), semi (1), fully (2) (default: 'fully' valid: 'non-enzy matic', '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 digesti on (default: '7' min: '0') -digest:max_length <digest_max_length> Maximum length of peptides to be generated during in-silico digesti on (default: '64' min: '0') -digest:mass_range_min <digest_mass_range_min> Min mass of peptides to be generat ed (Da) (default: '500' min: '0') -digest:mass_range_max <digest_mass_range_max> Max mass of peptides to be generat ed (Da) (default: '5000' min: '0') Variable Modification Parameters: -varmod:clip_nterm_m Specifies the trimming of a protei n N-terminal methionine as a varia ble modification -varmod:masses <varmod1_mass .. varmod7_mass> Masses for variable modifications -varmod:syntaxes <varmod1_syntax .. varmod7_syntax> Syntax Strings for variable modifi cations -varmod:enable_common Enable common variable modificatio ns (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 variabl e modifications -varmod:max_variable_mods_per_mod <max_variable_mods_per_mod> Maximum number of residues that can be occupied by each variable modification (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 experim ental spectrum for matching (defau lt: '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 experimen tal spectrum less intense than this multiple of the base peak intensity (default: '0' min: '0' max: '1') -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' min: '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' min: '0') -spectrum:max_fragment_charge <max_fragment_charge> Maximum charge state for theoretic al fragments to match (default: '2' valid: '1', '2', '3', '4') -spectrum:override_charge Ignores precursor charge and uses charge state specified in precurso r_charge range (parameters: spectr um:precursor_charge_min and spectr um: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 resul ts internally for boosting feature s. Should be set to a number great er 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 expecta tion less than this value (default : '0' min: '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' min: '0') -search:add_topn_complementary <add_topn_complementary> Inserts complementary ions corresp onding 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 statistica l 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 narr ow window searching and 6 for open searches (default: '4' min: '0') -search:output_report_topn <output_report_topn> Reports top N PSMs per input spect rum (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' min: '0') Static Modification Parameters: -statmod:add_cterm_peptide <add_cterm_peptide> Statically add mass in Da to C-ter minal of peptide (default: '0' min: '0') -statmod:add_nterm_peptide <add_nterm_peptide> Statically add mass in Da to N-ter minal of peptide (default: '0' min: '0') -statmod:add_cterm_protein <add_cterm_protein> Statically add mass in Da to C-ter minal of protein (default: '0' min: '0') -statmod:add_nterm_protein <add_nterm_protein> Statically add mass in Da to N-ter minal of protein (default: '0' min: '0') Common UTIL options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (defa ult: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advan ced)
INI file documentation of this tool: