[EMBOSS] Pepstats "Molecular weight" calculations

[Peter Rice]

CAPS (Carsten P. Sönksen) wrote:
> Hi
> We are using Pepstat for molecular weight calculations and subsequent
> comparison with mass spectrometric determined masses. I am looking for
> the mass table used for the molecular weight calculations of the
> proteins in order to determine the accuracy. And how it could be
> possible to change it.

The table is in a file called Emolwt.dat

This should be included in the local data files section of the pepstats 
documentation. We will add it. It is at least mentioned in the -help output 
and in the command line section of the documentation. The local data files 
section should describe the file in more detail.

A copy in your local diretcory (embossdata-fetch will copy the EMBOSS 
version for you) will be used in preference to the installed copy.

> The other question is implementation of a molecular weight assuming that
> the cysteins form disulfide bridges. This question is related to my
> first line. Since we compare the intact molecular weight of the proteins
> we want to be as precise as possible and thus measure the difference
> between reduced and oxidized cystein residues. Most proteins with
> cystein residues form disulfide bridges. Would it be possible to include
> a molecular weight calculation which takes disulfide bridges into
> account? So that an even nr of cysteins are calculated with the mass of
> oxidized  cysteins (S-S) and if there should be an single cystein left
> then it is calculated with a sulfhydryl group (SH)?

Good suggestion. We can add that for the next release. we would add an 
option for the number of S-S bridges and adjust the molecular weight.
We have a similar option already for iep.

Is there a need for single cysteines to allow for inter-chain disulphide 
bridges?

Are there any other adjustments you would like?

regards,

Peter Rice