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MetaboliteAdductDecharger

Decharges a feature map by clustering charge variants of metabolites to zero-charge entities.

pot. predecessor tools → MetaboliteAdductDecharger → pot. successor tools
FeatureFinderMetabo

The Decharger uses an ILP approach to group charge variants of the same metabolite, which usually occur in ESI ionization mode. The resulting zero-charge metabolites, 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 metabolites in each dimension (m and RT). For clustered metabolites, the reported m/z is thus their neutral mass. For unclusted features with known charge, a default adduct (protonation for positive mode, deprotonation for negative mode) is assumed to compute the neutral mass. For unclustered features without known charge, m/z zero is reported. 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 derived from the method 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: