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Update PSM level protein/master protein assignments using peptide-level assignments

update_peptide_assignments.Rd

When multiple search engines are used in Proteome Discoverer for TMT proteomics the PSM to protein and master protein assignments may not be consistent between the search engines. We can resolve this using the peptide level output from Proteome Discoverer, which has consistent assignments

Usage

update_peptide_assignments(
  obj,
  pep_inf,
  verbose = FALSE,
  master_protein_col = "Master.Protein.Accessions"
)

Arguments

obj

SummarisedExperiment containing PSM-level output from Proteome Discoverer.

pep_inf

string. Filepath for Peptide-level output

verbose

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

master_protein_col

string. Name of column containing master proteins. (Only used when verbose=TRUE)

Value

Returns a SummarisedExperiment with the standardised assignments

Details

Leucine/Isoleucine Leucine/Isoleucine are isobaric and only generate distinct fragments with higher collision energies which are not typically used in proteomics analysis. Thus, L and I are usually indistinguishable.

The spectrum search engines deal with this differently in terms of how they report the multiple possible sequence matches and their assignments.

The peptide level Proteome Discoverer output selects one possible sequence and uses the union of reported assignments from the PSM level for the peptide level assignments. Thus, when we use the peptide level assignments, we will lose PSM level data for the redundant sequences which were not selected. This is not an issue but will result in the function output being shorter than the input.