protViz (version 0.7.9)

aa2mass: 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.

Author

Christian Panse 2014

Details

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

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