[EMBOSS] Pepstats "Molecular weight" calculations
pmr at ebi.ac.uk
Tue Aug 25 12:56:30 UTC 2009
CAPS (Carsten P. Sönksen) wrote:
> 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
Are there any other adjustments you would like?
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