OpenMS
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Splits an mzML file with IonMobility frames into multiple mzML files by binning(merging) spectra by their IM values
Useful to convert IM data to a format that can be processed by tools that do not support IM data (e.g. FeatureFinderCentroided or SearchEngines). The results of individual bins can be processed separately and then recombined afterwards.
To decide on the number of bins, try running FileInfo on the input file to get an idea of the range of IM values present.
The command line parameters of this tool are:
IonMobilityBinning -- Splits an mzML file with IonMobility frames into multiple mzML files by binning(merging ) spectra by their IM values Full documentation: http://www.openms.de/doxygen/release/3.2.0/html/TOPP_IonMobilityBinning.html Version: 3.2.0 Sep 18 2024, 16:00:56, Revision: e231942 To cite OpenMS: + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7. Usage: IonMobilityBinning <options> Options (mandatory options marked with '*'): -in <file>* Input file (containing RT, IM, m/z, i.e. IM-frames). (valid formats: 'mzML') -out <directory>* Path to the output directory to write the binned mzML files to. -bins <number> Number of ion mobility bins to split the input file into (def ault: '5') -bin_extension_abs <number> Absolute extension of the bin in IM dimension (causes bins to overlap by 2x this value) (default: '0.0') Options for merging spectra within the same IM bin (from the same IM-frame): -SpectraMerging:mz_binning_width <number> Width of the m/z bins (default: '0.01') -SpectraMerging:mz_binning_width_unit <unit> Unit of the m/z bin width (default: 'Da') (valid: 'Da', 'ppm' ) 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: