OpenMS
2.5.0
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Corrects the precursor mz of high resolution data.
pot. predecessor tools | HighResPrecursorMassCorrector | pot. successor tools |
PeakPickerHiRes | MascotAdapter (or other ID engines) |
This tool performs precursor m/z correction on picked (=centroided) high resolution data.
Three methods are available: 'nearest_peak', 'highest_intensity_peak' and 'feature'.
The method hightest_intensity_peak searches in a specific m/z-window of the precursor information for the peak with the highest intensity. Suggestioned value 1/maximal expected charge. E.g maximal expected charge 5, m/z-window = +/- 0.2 Da
See the corresponding parameter subsection for details.
The command line parameters of this tool are:
HighResPrecursorMassCorrector -- Corrects the precursor mass and charge determined by the instrument software . Full documentation: http://www.openms.de/documentation/TOPP_HighResPrecursorMassCorrector.html Version: 2.5.0-nightly-2020-03-06 Mar 7 2020, 01:22:16, Revision: 84b1398 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. Usage: HighResPrecursorMassCorrector <options> Options (mandatory options marked with '*'): -in <file>* Input file (centroided data) (valid formats: 'mzML') -out <file>* Output file (valid formats: 'mzML') Use features for precursor mass correction.: -feature:in <file> Features used to correct precursor masses. (valid forma ts: 'featureXML') -feature:mz_tolerance <num> The precursor mass tolerance. Used to determine matchin g to feature mass traces. (default: '5.0') -feature:mz_tolerance_unit <choice> Unit of precursor mass tolerance (default: 'ppm' valid: 'Da', 'ppm') -feature:rt_tolerance <num> Additional retention time tolerance added to feature boundaries. (default: '0.0') -feature:believe_charge Assume precursor charge to be correct. -feature:keep_original Make a copy of the precursor and MS2 (true) or discard the original (false). -feature:assign_all_matching Correct a precursor using all matching features (true) or only the nearest (false). Only evaluated if copies are created (feature:keep_original). Use nearest centroided MS1 peak for precursor mass correction.: -nearest_peak:mz_tolerance <num> The precursor mass tolerance to find the closest MS1 peak. (Disable method by setting value to 0.0) (default : '0.0') -nearest_peak:mz_tolerance_unit <choice> Unit of precursor mass tolerance (default: 'ppm' valid: 'Da', 'ppm') Use centroided MS1 peak with the highest intensity in a certrain mass range - for precursor mass correction: -highest_intensity_peak:mz_tolerance <num> The precursor mass tolerance to find the highest intens ity MS1 peak. Suggested value 1/max. expected charge. (Disable method by setting value to 0.0) (default: '0.0 ') -highest_intensity_peak:mz_tolerance_unit <choice> Unit of precursor mass tolerance (default: 'ppm' valid: 'Da', 'ppm') -out_csv <file> Optional CSV output file for results on 'nearest_peak' or 'highest_intensity_peak' algorithm (see correspondin g subsection) containing columns: RT, uncorrectedMZ, correctedMZ, deltaMZ. (valid formats: 'csv') 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: