silac_psm_seq_int: Extract peptide sequencing and interference information from...

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

Extract peptide sequencing and interference information from SILAC PSM-level output

Description

Proteome Discoverer does not correctly propagate from PSM to peptide level output which intensities are from "matched" peptides, e.g MS2 fragmentation. This information is useful to assess the accuracy of quantification in peptides identified by mass shift relative to a matched peptide in SILAC experiments

Usage

silac_psm_seq_int(
  obj,
  sequence_col = "Sequence",
  mod_col = "Modifications",
  include_interference = FALSE,
  interference_col = "Isolation.Interference.in.Percent",
  group_cols = NULL,
  psm_modfication_regexes = c(get_psm_silac_mod_regex("R_13C6_15N4"),
    get_psm_silac_mod_regex("K_13C6_15N2"))
)

Arguments

obj	data.frame PSM-level output from Proteome Discoverer
sequence_col	string Column with peptide sequence
mod_col	string Column with modifications
include_interference	logical Should PSM interference be included too?
interference_col	string Column with interference/co-isolation
group_cols	string Additional feature columns to retain, beyond
psm_modfication_regexes	character vector One or more regexes to match the expected SILAC modifications Sequence and Modification. See get_psm_silac_mod_regex

Value

data.frame indicating which SILAC peptides were MS2 matched, how many PSMs per isotope, and (optionally) the maximum interference across all PSMs for the peptide

CambridgeCentreForProteomics/camprotR documentation built on Jan. 27, 2023, 8:36 p.m.