[BioC] Protein/peptide mass

[Sean Davis]

On 5/25/06 4:07 AM, "john seers (IFR)" <john.seers at bbsrc.ac.uk> wrote:

> 
> 
> Hi Thomas
> 
> Thank you very much for your reply.
> 
> There are some functions in the packages "seqinr" and "Biostrings", in
> fact quite a lot, but not one to calculate the mass of a peptide that I
> can find. So I was being forced down the route of having to call an
> EMBOSS program and parse the results. The problem with that is the
> interface is not easy - often needs a file as input in some standard
> format - not just passing in a string on the command line.
> 
> The other way I thought might be possible was to use the online
> facilities of something like Expasy's "PeptideMass" but I cannot get
> that to work. Does anybody have any idea if that is possible?

How precise do you want to be?  Here is an online table of masses for each
AA.  You could some of the facilities in Biostrings to do the AA counting
and then multiply the counts by the weights to get something approximating
the real value.  See here:

http://www.gla.ac.uk/cancerpathology/genemech/awest/Prot_calc.htm

Sean