Required columns are "fc.raw.file", "modified.sequence" and "is.transferred".
getPeptideCounts(df_evd)Data.frame of evidence.txt as read by MQDataReader
Data.frame with columns 'fc.raw.file', 'counts', 'category', 'MBRgain'
If match-between-runs was enabled during the MaxQuant run, the data.frame returned will contain separate values for 'transferred' evidence plus an 'MBRgain' column, which will give the extra MBR evidence in percent.