add_mod_symbol: Annotates peptide sequences with modification symbols

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

Description

Given the provided modification mass, annotates its position within the peptide sequence with provided symbol.

Usage

    add_mod_symbol(object, mod_mass, symbol)

Arguments

object	An instance of class "MSnID".
mod_mass	(string) modification mass. Must match exactly one of the masses in report_mods.
symbol	(string) character that annotates the position of the modification

Value

Returns MSnID object with new or modified peptide_mod column. The column contains peptide sequence with amino acid modifications annotated with symbols.

Note

In current implementation the method can not distinguish modifications with the same mass, but different amino acid specificity as different modifications.

Author(s)

Vladislav A Petyuk [e-mail]

See Also

report_mods map_mod_sites

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"))))

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

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