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

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

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