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Remove redundant Peptide Spectrum Matches

remove_redundant_psm_quant.Rd

When multiple search engines are used in Proteome Discoverer for TMT proteomics, the PSM-level quantification contains duplicate rows for each search engine match to the same spectrum. We can use the scan number columns and quantitative data to identify the duplicate rows and exclude them.

The removal of duplicate quantification should be performed following initial filtering to 1) remove rejected PSMs (see filter_TMT_PSMs) and 2) retain only rank 1 matches (Filter on Rank and Search.Engine.Rank columns)

Usage

remove_redundant_psm_quant(
  obj,
  verbose = FALSE,
  master_protein_col = "Master.Protein.Accessions",
  validate = TRUE
)

Arguments

obj

SummarisedExperiment containing PSM-level output from Proteome Discoverer.

verbose

boolean. Don't output tallies of PSMs/proteins; Default=FALSE

master_protein_col

string. Name of column containing master

validate

logical. Check that sequence to protein assignments are consistent. Default=TRUE proteins. (Only used when verbose=TRUE)

Value

Returns a SummarisedExperiment with the redundant quantification removed