OpenMS
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MaRaClusterAdapter facilitates the input to, the call of and output integration of MaRaCluster. MaRaCluster (https://github.com/statisticalbiotechnology/maracluster) is a tool to apply unsupervised clustering of ms2 spectra from shotgun proteomics datasets.
pot. predecessor tools | → MaRaClusterAdapter → | pot. successor tools |
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any signal-/preprocessing tool (in mzML format) | MSGFPlusAdapter |
MaRaCluster is dependent on the input parameter pcut, which is the logarithm of the pvalue cutoff. The default value is -10, lower values will result in smaller but purer clusters. If specified peptide search results can be provided as idXML files and the MaRaCluster Adapter will annotate cluster ids as attributes to each peptide identification, which will be outputed as a merged idXML. Moreover the merged idXML containing only scan numbers, cluster ids and file origin can be outputed without prior peptide identification searches. The assigned cluster ids in the respective idXML are equal to the scanindex of the produced clustered mzML.
The command line parameters of this tool are:
MaRaClusterAdapter -- Facilitate input to MaRaCluster and reintegrate. Full documentation: http://www.openms.de/doxygen/release/3.2.0/html/TOPP_MaRaClusterAdapter.html Version: 3.2.0 Nov 26 2024, 13:16:38, Revision: 962e60f 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. To cite MaRaClusterAdapter: + The M and Käll L. MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteo mics. J Proteome Res 2016; 15: 3. doi:10.1021/acs.jproteome.5b00749. Usage: MaRaClusterAdapter <options> Options (mandatory options marked with '*'): -in <files>* Input file(s) (valid formats: 'mzML', 'mgf') -id_in <files> Optional idXML Input file(s) in the same order as mzML files - for Maracluster Cluster annotation (valid formats: 'idXML') -out <file> Output file in idXML format (valid formats: 'idXML') -consensus_out <file> Consensus spectra in mzML format (valid formats: 'mzML') -output_directory <directory> Output directory for MaRaCluster original consensus output -pcut <value> Log(p-value) cutoff, has to be < 0.0. Default: -10.0. (default: '-10 .0') (max: '0.0') -min_cluster_size <value> Minimum number of spectra in a cluster for consensus spectra (defaul t: '1') (min: '1') -maracluster_executable <executable>* The maracluster executable. Provide a full or relative path, or make sure it can be found in your PATH environment. 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 (defa ult: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced)
INI file documentation of this tool:
MaRaCluster is written by Matthew The (https://github.com/statisticalbiotechnology/maracluster Copyright Matthew The matth) Cite Publication: MaRaCluster: A Fragment Rarity Metric for Clustering Fragment Spectra in Shotgun Proteomics Journal of proteome research, 2016, 15(3), pp 713-720 DOI: 10.1021/acs.jproteome.5b00749 ew.t he@sc ilif elab. se