remove_silac_modifications: Remove SILAC labels from modifications

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

Remove SILAC labels from modifications

Description

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.

Usage

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

CambridgeCentreForProteomics/camprotR documentation built on July 7, 2024, 2:13 a.m.