Extracts portions of the data from an mzML, featureXML or consensusXML file.
pot. predecessor tools | ![]() ![]() | pot. successor tools |
any tool yielding output in mzML, featureXML or consensusXML format | any tool that profits on reduced input |
With this tool it is possible to extract m/z, retention time and intensity ranges from an input file and to write all data that lies within the given ranges to an output file.
Depending on the input file type, additional specific operations are possible:
The priority of the id-flags is (decreasing order): remove_annotated_features / remove_unannotated_features -> remove_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist
MS2 and higher spectra can be filtered according to precursor m/z (see 'pc_mz'). This flag can be combined with 'rt' range to filter precursors by RT and m/z. If you want to extract an MS1 region with untouched MS2 spectra included, you will need to split the dataset by MS level and use 'mz' option for MS1 and 'pc_mz' for MS2 data. Then merge them again. RT can be filtered at any step.
The command line parameters of this tool are:
FileFilter -- Extracts or manipulates portions of data from peak, feature or consensus-feature files. Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976 Usage: FileFilter <options> This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti on or use the --helphelp option. Options (mandatory options marked with '*'): -in <file>* Input file (valid formats: 'mzML', 'featureXML', 'cons ensusXML') -in_type <type> Input file type -- default: determined from file extens ion or content (valid: 'mzML', 'featureXML', 'consensusXML') -out <file>* Output file (valid formats: 'mzML', 'featureXML', 'cons ensusXML') -out_type <type> Output file type -- default: determined from file exten sion or content (valid: 'mzML', 'featureXML', 'consensusXML') -rt [min]:[max] Retention time range to extract (default: ':') -mz [min]:[max] M/z range to extract (applies to ALL ms levels!) (defau lt: ':') -pc_mz [min]:[max] MSn (n>=2) precursor filtering according to their m/z value. Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compati ble with this flag. (default: ':') -int [min]:[max] Intensity range to extract (default: ':') -sort Sorts the output according to RT and m/z. Peak data options: -peak_options:sn <s/n ratio> Write peaks with S/N > 'sn' values only (default: '0') -peak_options:rm_pc_charge i j ... Remove MS(2) spectra with these precursor charges. All spectra without precursor are kept! -peak_options:level i j ... MS levels to extract (default: '[1 2 3]') -peak_options:sort_peaks Sorts the peaks according to m/z. -peak_options:no_chromatograms No conversion to space-saving real chromatograms, e.g. from SRM scans. -peak_options:remove_chromatograms Removes chromatograms stored in a file. -peak_options:mz_precision 32 or 64 Store base64 encoded m/z data using 32 or 64 bit precis ion. (default: '64' valid: '32', '64') -peak_options:int_precision 32 or 64 Store base64 encoded intensity data using 32 or 64 bit precision. (default: '32' valid: '32', '64') Remove spectra or select spectra (removing all others) with certain properties.: -spectra:remove_zoom Remove zoom (enhanced resolution) scans -spectra:remove_mode <mode> Remove scans by scan mode (valid: 'Unknown', 'MassSpectrum', 'MS1Spectrum', 'MS nSpectrum', 'SelectedIonMonitoring', 'SelectedReactionM onitoring', 'ConsecutiveReactionMonitoring', 'ConstantN eutralGain', 'ConstantNeutralLoss', 'Precursor', 'Enhan cedMultiplyCharged', 'TimeDelayedFragmentation', 'Elect romagneticRadiation', 'Emission', 'Absorbtion') Remove spectra or select spectra (removing all others) with certain properties.: -spectra:remove_activation <activation> Remove MSn scans where any of its precursors features a certain activation method (valid: 'Collision-induced dissociation', 'Post-sourc e decay', 'Plasma desorption', 'Surface-induced dissoci ation', 'Blackbody infrared radiative dissociation', 'Electron capture dissociation', 'Infrared multiphoton dissociation', 'Sustained off-resonance irradiation', 'High-energy collision-induced dissociation', 'Low-ener ... ion') -spectra:remove_collision_energy [min]:[max] Remove MSn scans with a collision energy in the given interval. (default: ':') -spectra:remove_isolation_window_width [min]:[max] Remove MSn scans whichs isolation window width is in the given interval. (default: ':') Remove spectra or select spectra (removing all others) with certain properties.: -spectra:select_zoom Select zoom (enhanced resolution) scans -spectra:select_mode <mode> Selects scans by scan mode (valid: 'Unknown', 'MassSpectrum', 'MS1Spectrum', 'MS nSpectrum', 'SelectedIonMonitoring', 'SelectedReactionM onitoring', 'ConsecutiveReactionMonitoring', 'ConstantN eutralGain', 'ConstantNeutralLoss', 'Precursor', 'Enhan cedMultiplyCharged', 'TimeDelayedFragmentation', 'Elect romagneticRadiation', 'Emission', 'Absorbtion') -spectra:select_activation <activation> Select MSn scans where any of its precursors features a certain activation method (valid: 'Collision-induced dissociation', 'Post-sourc e decay', 'Plasma desorption', 'Surface-induced dissoci ation', 'Blackbody infrared radiative dissociation', 'Electron capture dissociation', 'Infrared multiphoton dissociation', 'Sustained off-resonance irradiation', 'High-energy collision-induced dissociation', 'Low-ener ... ion') -spectra:select_collision_energy [min]:[max] Select MSn scans with a collision energy in the given interval. (default: ':') -spectra:select_isolation_window_width [min]:[max] Select MSn scans whichs isolation window width is in the given interval. (default: ':') Feature data options: -feature:q [min]:[max] Overall quality range to extract [0:1] (default: ':') Consensus feature data options: -consensus:map i j ... Maps to be extracted from a consensus -consensus:map_and Consensus features are kept only if they contain exactl y one feature from each map (as given above in 'map'). Black or white listing of of MS2 spectra by consensus features.: -consensus:blackorwhitelist:blacklist True: remove matched MS2. False: retain matched MS2 spectra. Other levels are kept. (default: 'true' valid: 'false', 'true') -consensus:blackorwhitelist:file <file> Input file containing consensus features whose correspo nding MS2 spectra should be removed from the mzML file! Matching tolerances are taken from 'consensus:blackorw hitelist:rt' and 'consensus:blackorwhitelist:mz' option s. If consensus:blackorwhitelist:maps is specified, only these will be used. (valid formats: 'consensusXML') -consensus:blackorwhitelist:maps i j ... Maps used for black/white list filtering. -consensus:blackorwhitelist:rt tolerance Retention tolerance [s] for precursor to consensus feat ure position (default: '60' min: '0') -consensus:blackorwhitelist:mz tolerance M/z tolerance [Th] for precursor to consensus feature position (default: '0.01' min: '0') -consensus:blackorwhitelist:use_ppm_tolerance If ppm tolerance should be used. Otherwise Da are used. (default: 'false' valid: 'false', 'true') Feature & Consensus data options: -f_and_c:charge [min]:[max] Charge range to extract (default: ':') -f_and_c:size [min]:[max] Size range to extract (default: ':') -f_and_c:remove_meta <name> 'lt|eq|gt' <value> Expects a 3-tuple (=3 entries in the list), i.e. <name> 'lt|eq|gt' <value>; the first is the name of meta valu e, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corres ponding data value type of the meta value (for lists, this simply compares length, not content!)! ID options. The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -> remov e_clashes -> keep_best_score_id -> sequences_whitelist / accessions_whitelist.: -id:keep_best_score_id In case of multiple peptide identifications, keep only the id with best score -id:sequences_whitelist <sequence> Keep only features with white listed sequences, e.g. LYSNLVER or the modification (Oxidation) -id:accessions_whitelist <accessions> Keep only features with white listed accessions, e.g. sp|P02662|CASA1_BOVIN -id:remove_annotated_features Remove features with annotations -id:remove_unannotated_features Remove features without annotations -id:remove_unassigned_ids Remove unassigned peptide identifications -id:blacklist <file> Input file containing MS2 identifications whose corresp onding MS2 spectra should be removed from the mzML file ! Matching tolerances are taken from 'id:rt' and 'id:mz' options. This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:black list_imperfect' to allow for mismatches. (valid formats : 'idXML') -id:rt tolerance Retention tolerance [s] for precursor to id position (default: '0.1' min: '0') -id:mz tolerance M/z tolerance [Th] for precursor to id position (defaul t: '0.001' min: '0') -id:blacklist_imperfect Allow for mismatching precursor positions (see 'id:blac klist') 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) The following configuration subsections are valid: - algorithm S/N algorithm section You can write an example INI file using the '-write_ini' option. Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor. Have a look at the OpenMS documentation for more information.
INI file documentation of this tool:
For the parameters of the S/N algorithm section see the class documentation there:
peak_options:sn
OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5 |