read psm.tsv produced by FragPipe and convert into long format

Usage

tidy_FragPipe_psm(
  psm_files,
  purity_threshold = 0.5,
  PeptideProphetProb = 0.9,
  abundance_threshold = 0,
  column_before_quants = c("Quan Usage", "Mapped Proteins"),
  aggregate = TRUE
)

Arguments

psm_files: path(s) to psm.tsv file(s)
purity_threshold: purity threshold default = 0.5
PeptideProphetProb: default 0.9
abundance_threshold: minimum abundance threshold
column_before_quants: describes the last column before the quantitative values (this is not consistent with in different versions of FP, default "Quan Usage"
aggregate: aggregate spectra to psm level