extract_sequence_window: Extracts +/-7 amino acids to the PTM

In vladpetyuk/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 7 amino acids to the left and right of each PTM, with "-" character appended if PTM is near start or end of protein sequence. The modified AA is turned into lowercase.

Usage

    extract_sequence_window(object,
                           fasta,
                           accession_col="accession",
                           site_loc_col="SiteLoc",
                           radius=7L,
                           collapse="|")

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	(character) Name of accession column.
site_loc_col	(character) Name of column containing site locations.
radius	(integer) How many amino acids to map to left and right of the PTM.
collapse	(character) Symbol to separate multiple PTMs.

Value

MSnID object with an extra column sequenceWindow giving the neighborhood of each PTM.

Author(s)

Michael Nestor [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")

# # mapping +/-7 amino acids to the PTm
m <- extract_sequence_window(m, fst)

head(unique(subset(psms(m), select=c("accession", "peptide", "sequenceWindow"))))

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

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