The Decharger uses a hierarchical clustering (complete linkage) 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 a featureXML file. Intensities of charge variants are summed up. The position of the zero charge variant is the average of all clustered peptides in each dimension. If several peptides with the same charge variant are grouped (which is clearly not allowed), a heuristic is used:
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