locatePTM: Annotate modified sites with associated peptides

In Vitek-Lab/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Annotate modified sites with associated peptides

Description

PTMlocate annotates modified sites with associated peptides.

Usage

locatePTM(peptide, uniprot, fasta, modResidue, modSymbol, rmConfound = FALSE)

Arguments

peptide	A string vector of peptide sequences. The peptide sequence does not include its preceding and following AAs.
uniprot	A string vector of Uniprot identifiers of the peptides' originating proteins. UniProtKB entry isoform sequence is used.
fasta	A tibble with FASTA information. Output of tidyFasta.
modResidue	A string. Modifiable amino acid residues.
modSymbol	A string. Symbol of a modified site.
rmConfound	A logical. TRUE removes confounded unmodified sites, FALSE otherwise. Default is FALSE.

Value

A data frame with three columns: uniprot_iso, peptide, site.

Examples

fasta <- tidyFasta(system.file("extdata", "O13297.fasta", package="MSstatsLiP"))
locatePTM("DRVSYIHNDSC*TR", "O13297", fasta, "C", "\\*")

Vitek-Lab/MSstatsLiP documentation built on April 5, 2024, 3:25 a.m.