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
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