The spectralCount is used only for selecting representative proteoform for a feature cluster. Note the cluster may contain proteoforms annotated with shorter and longer sequences and different modification masses (due to the imperfections in the mass spectra interpretation). Thus the actual count the proteoform defined by the combination of gene and pcGroup (proteoform cluster) combination is actually higher.
spectralCount better be removed from the x_meta object to avoid downstream confusion.
https://github.com/PNNL-Comp-Mass-Spec/TopPICR/blob/e77cf600fa276d3d8f4b4de6ed228989fe752fe9/R/create_metadata.R#L75
The
spectralCountis used only for selecting representative proteoform for a feature cluster. Note the cluster may contain proteoforms annotated with shorter and longer sequences and different modification masses (due to the imperfections in the mass spectra interpretation). Thus the actual count the proteoform defined by the combination of gene and pcGroup (proteoform cluster) combination is actually higher.spectralCountbetter be removed from thex_metaobject to avoid downstream confusion.