There exist peptides annotated as protein groups with 2/ProteinA/DECOY_ProteinB. However these are in principal proteotypic peptides and should be annoated 1/ProteinA. This function changes these labels accordingly. The subfunction rmDecoyProt removes the Decoy protein, calling removeDecoyProteins also changes the nubmer before the protein group accordingly.
A data frame containing SWATH data.
Column to query for decoy string
String defining a decoy. Default: DECOY
Returns a data frame with changed protein labels
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