map_mod_sites {MSnID} | R Documentation

## Maps the modifications to protein sequence

### 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 vladislav.petyuk@pnnl.gov

### 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)

[Package MSnID version 1.28.0 Index]