R: determine the weight if a fiven amino acid sequence

aa2mass {protViz} | R Documentation

## determine the weight if a fiven amino acid sequence

### Description

The function determines the weight of each amino acid fiven sequence.

### Usage

        aa2mass(peptideSequence, mass=AA$Monoisotopic, letter1=AA$letter1)

### Arguments

`peptideSequence` | a double vector which can be considered as query objects.
`mass` | A vector of size 20 containing the weight of the AA.
`letter1` | AA letter 1 code in the same size and order as the `mass` attribute.

### Details

For the computation no C-Term and N-Term is considered. `aa2mass` is useful if you have AA modifications.

### Author(s)

Christian Panse 2014

### Examples

        peptides<-c('HTLNQIDSVK', 'ALGGEDVR', 'TPIVGQPSIPGGPVR')

        C_term <- 17.002740
        N_term <- 1.007825
        H_ <- 1.008

        unlist(lapply(aa2mass(peptides), sum)) + C_term + N_term + H_ - parentIonMass(peptides)

        # determine the fragment ions
        lapply(aa2mass(peptides), function(x){fragmentIon(x)[[1]]})

        # an example with [STY] AA modification

        peptide<-'HTLNQIDSVK'
        mod <- rep(0.0, nchar(peptide)); mod[8] <- 79.998;

        aa2mass(peptide)[[1]] + mod

[Package protViz version 0.6.8 Index]