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MaRaClusterAdapter

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.

Experimental classes:
This tool is work in progress and usage and input requirements might change.
pot. predecessor tools → MaRaClusterAdapter → pot. successor tools
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:

INI file documentation of this tool:

MaRaCluster is written by Matthew The (https://github.com/statisticalbiotechnology/maracluster Copyright Matthew The matth.nosp@m.ew.t.nosp@m.he@sc.nosp@m.ilif.nosp@m.elab..nosp@m.se) 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