Remove SILAC labels from modifications

This function removes SILAC heavy/light labels from a PD Modifications column. When dealing with PSM level Proteome Discoverer output, this is required to match PSMs for the same peptide, or to transfer PSM-level features to peptide-level data.

remove_silac_modifications(
  mod_col,
  level = "psm",
  psm_modfication_regexes = c(get_psm_silac_mod_regex("R_13C6_15N4"),
    get_psm_silac_mod_regex("K_13C6_15N2"))
)

Arguments

mod_col

character vector Modification column from Proteome Discoverer

level

character Either 'psm' or 'peptide'

psm_modfication_regexes

character vector One or more regexes to match the expected SILAC modifications. See get_psm_silac_mod_regex

Value

character vector updated Modifications column