OpenMS
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Cluster mass traces occurring in the same map together
Cluster mass traces together found in a mass spectrometric map (MS1 or MS2). Input is a consensus map containing individual mass traces, the output may be spectra containing all clustered features.
Mass traces are clustered independent of precursor traces in another map (this is the more simple approach) and pseudo spectra are created without any precursors assigned. This is useful for
On the clustered fragments in an MS2 map, one can then (optionally) do
The command line parameters of this tool are:
ClusterMassTraces -- Creates pseudo spectra. Full documentation: http://www.openms.de/doxygen/release/3.2.0/html/TOPP_ClusterMassTraces.html Version: 3.2.0 Nov 18 2024, 16:14:00, Revision: 03223c3 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: ClusterMassTraces <options> Options (mandatory options marked with '*'): -in <file>* Mass traces (valid formats: 'consensusXML') -out <file>* Output file (valid formats: 'mzML') -min_pearson_correlation <double> Minimal pearson correlation score (default: '0.7') -min_peak_nr <number> Minimal peak nr to output pseudo spectra (default: '1') -max_lag <number> Maximal lag (default: '1') -max_rt_apex_difference <double> Maximal difference of the apex in retention time (default: '5.0') -max_intensity_cutoff <double> Maximal intensity to be added to a spectrum (default: '0.0') -add_precursor <double> Add a precursor mass (default: '0.0') 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: