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OpenMS
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Decharges a feature map by clustering charge variants of a peptide to zero-charge entities.
pot. predecessor tools | → Decharger → | pot. successor tools |
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FeatureFinderCentroided | ProteinQuantifier |
The Decharger uses an ILP approach to group charge variants of the same peptide, which usually occur in ESI ionization mode. The resulting zero-charge peptides, which are defined by RT and mass, are written to consensusXML. Intensities of charge variants are summed up. The position of the zero charge variant is the average of all clustered peptides in each dimension (m/z and RT). It is also possible to include adducted species to the charge ladders (see 'potential_adducts' parameter). Via this mechanism it is also possible to use this tool to find pairs/triples/quadruples/... in labeled data (by specifing the mass tag weight as an adduct). If mass tags induce an RT shift (e.g. deuterium labeled data) you can also specify this also in the adduct list. This will allow to tighten the RT search window, thus reducing false positive results.
This tool is described in the following publication:
Bielow C, Ruzek S, Huber CG, Reinert K. Optimal decharging and clustering of charge ladders generated in ESI-MS. J Proteome Res 2010; 9: 2688.
DOI: 10.1021/pr100177k
The command line parameters of this tool are:
INI file documentation of this tool: