[BioC] Protein/peptide mass

[john seers (IFR)]

Hi Sean

Thanks for the reply and the web page information.

I need to be quite precise and I will need the variations for post
translational modifications and other options. E.g. monoisotopic vs
average. (Not sure exactly what I need yet).

I guess I can do it myself but it is quite a lot of work to find and
understand all the variations and test it. More the problem is that I do
not really want to reinvent the wheel. I was quite surprised I cannot
find a module to do it - I thought I was just not looking in the right
place. I can find isoelectric points, hydropathy plots etc etc but no
mass/Mw calculator. 

Regards

John Seers










 
---

John Seers
Institute of Food Research
Norwich Research Park
Colney
Norwich
NR4 7UA
 

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-----Original Message-----
From: Sean Davis [mailto:sdavis2 at mail.nih.gov] 
Sent: 25 May 2006 12:01
To: john seers (IFR); Thomas Girke
Cc: Bioconductor
Subject: Re: [BioC] Protein/peptide mass





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