map_mod_sites: Maps the modifications to protein sequence

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

Description

Given the peptide sequence with modification X.XXXX*XXXX.X and provided protein sequence FASTA, the method maps the location of the modification resulting in {protein ID}-{aa}{aa position}".

Usage

    map_mod_sites(object,
                  fasta, 
                  accession_col = "accession", 
                  peptide_mod_col = "peptide_mod", 
                  mod_char = "*",
                  site_delimiter = "lower")

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".
peptide_mod_col	(string) Name of the column with modified peptide sequences in the MSnID object. Default is "peptide_mod".
mod_char	(string) character that annotates the position of the modification. Default is "*".
site_delimiter	(string) either a single character or "lower" (default) meaning it will be the same amino acid symbol, but in lower case

Value

MSnID object with extra columns regarting the modification mapping. Most likely, what you need is SiteID.

PepLoc	(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.
PepLocFirst	(int) position of the first occurence of the matching sequence
ProtLength	(int) protein length
ModShift	(vector of ints) positions of modified amino acids within peptide
ModAAs	(vector of characters) single-letter amino acid codes of the modified residues
SiteLoc	(list of vectors of ints) positions of the modified amino acids within protein for each occurence of the peptide
Site	(list of vectors of characters) modified sites encoded as amino acid symbol follwed by position for each occurence of the peptide
SiteCollapsed	(list of characters) same as Site, but modified sites for each peptide occurence collapsed into one string
SiteCollapsedFirst	(character) first element of the SiteCollapsed list
SiteID	(character) accession ID concatenated with SiteCollapsedFirst

Author(s)

Vladislav A Petyuk [e-mail]

Examples

m <- MSnID(".")
mzids <- system.file("extdata","phospho.mzid.gz",package="MSnID")
m <- read_mzIDs(m, mzids)

# to know the present mod masses
report_mods(m)

# TMT modification
m <- add_mod_symbol(m, mod_mass="229.1629", symbol="#")
# alkylation
m <- add_mod_symbol(m, mod_mass="57.021463735", symbol="^")
# phosphorylation
m <- add_mod_symbol(m, mod_mass="79.966330925", symbol="*")

# show the mapping
head(unique(subset(psms(m), select=c("modification", "peptide_mod"))))

# read fasta for mapping modifications
fst_path <- system.file("extdata","for_phospho.fasta.gz",package="MSnID")
library(Biostrings)
fst <- readAAStringSet(fst_path)
# to ensure names are the same as in accessions(m)
names(fst) <- sub("(^[^ ]*) .*$", "\1", names(fst))
# # mapping phosphosites
m <- map_mod_sites(m, fst, "accession", "peptide_mod", "*", "lower")

head(unique(subset(psms(m), select=c("accession", "peptide_mod", "SiteID"))))

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

MSnID documentation built on Nov. 8, 2020, 8:03 p.m.