map_peptide_position: Maps the peptide location(s) to protein sequence

In vladpetyuk/MSnID: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics Identifications

Description

The method maps the location of the modification resulting in {protein ID}-{aa}{aa position}.

Usage

    map_peptide_position(object,
                        fasta, 
                        accession_col = "accession")

Arguments

object	An instance of class MSnID.
fasta	(AAStringSet object) Protein sequences read from a FASTA file. Names must match protein/accesison IDs in the accesson column of the MSnID object.
accession_col	(string) Name of the column with accession/protein IDs in the MSnID object. Default is "accession".

Value

MSnID object with extra columns regarting the peptide location.

cleanSeq	(character) peptide sequence without modification characters and flanking amino acids
First_AA	(list of ints) position of the starting amino acid within protein sequence. It is a list, because there may be multiple occurences of the same sequence matching the peptide's sequence.
Last_AA	(list of ints) Same as First_AA, but last amino acid
First_AA_First	(int) First element of First_AA. Essentially, a first occurence of the peptide in the sequence.
Last_AA_First	(int) First element of Last_AA.

Author(s)

Vladislav A Petyuk [e-mail]

Examples

m <- MSnID(".")
mzids <- system.file("extdata","phospho.mzid.gz",package="MSnID")
m <- read_mzIDs(m, mzids)
fst_path <- system.file("extdata","for_phospho.fasta.gz",package="MSnID")
library(Biostrings)
fst <- readAAStringSet(fst_path)
# ensure names are the same format as accessions(m)
names(fst) <- sub("(^[^ ]*) .*$", "\1", names(fst))

# Creating sequences with repeats. This is just for the sake of 
# demonstration of the capability.
for(i in 2:4){
    fst[i] <- paste0(as.character(fst[i]),as.character(fst[i]))
}

# Appending reverse hits. Also, just for the demonstrating the capability.
mr <- mf <- apply_filter(m, "!isDecoy")
library(stringi)
mr$peptide <- stringi::stri_reverse(mr$peptide)
mr$accession <- paste0("XXX_", mr$accession)
mr$isDecoy <- TRUE
psms(m) <- rbind(psms(mr), psms(mf))

# the main call
m2 <- map_peptide_position(m, fst)

head(unique(subset(psms(m2), select=c("accession", 
                                      "peptide", 
                                      "First_AA",
                                      "First_AA_First",
                                      "Last_AA",
                                      "Last_AA_First",
                                      "ProtLen"))))

# clean-up cache
unlink(".Rcache", recursive=TRUE)

vladpetyuk/MSnID documentation built on June 25, 2021, 6:35 a.m.