I have a matrix for whole cell mass spectrometry data. I found that many rows have more than one protein. I am new to proteomics. May I ask the reason behind this?
It is a multimapper. Mass spec involves digestion of proteins into peptides first before running HPLC and the actual MS. If several proteins have conserved/similar/same peptide sequences then they can map ambiguously. In typical RNA-seq and similar assays multimappers are often discarded. Your choice what you do.
