aa2mass | R Documentation |
The function determines the weight of each amino acid fiven sequence.
aa2mass(peptideSequence, mass=AA$Monoisotopic, letter1=AA$letter1)
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 |
For the computation no C-Term and N-Term is considered.
aa2mass
is useful if you have AA modifications.
Christian Panse 2014
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
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