genMod: Generates all possible modification of a given peptide...

In protViz/protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Generates all possible modification of a given peptide seqence and modification pattern

Description

This function can be used to screen precursor masses for meaningful mass shifts which could correspond to post translational modifications. We suggest to only use a maxiumum of a handful of mass shifts.

Usage

    genMod(sequences, modificationPattern, nModification=2)

Arguments

sequences	peptide sequences encoded as character sequence using the 20 amino acid letters.
modificationPattern	a rbind list structure containing the mono and avg mass as well as the description of a the modifications.
nModification	number of maximal modifications.

Details

t.b.d.

Author(s)

Hubert Rehrauer and Christian Panse 2012

Examples

    ptm.0<-cbind(AA="-",
        mono=0.0, avg=0.0, desc="unmodified", unimodAccID=NA)

    ptm.616<-cbind(AA='S',
        mono=-27.010899, avg=NA, desc="Substituition",
            unimodAccID=616)

    ptm.651<-cbind(AA='N',
        mono=27.010899, avg=NA, desc="Substituition",
            unimodAccID=651)


    m<-as.data.frame(rbind(ptm.0, ptm.616, ptm.651))

    genMod(c('TAFDEAIAELDTLNEESYK','TAFDEAIAELDTLSEESYK'), m$AA)

protViz/protViz documentation built on Jan. 19, 2024, 8:10 a.m.