[EMBOSS] Pepstats "Molecular weight" calculations

[CAPS (Carsten P. Sönksen)]

Hi Peter,

Thanks a lot for fast and positive reply.

Regarding the molecular weight calculation including the disulfide bridges:
Would it be possible to have the option that pepstat always calculates the molecular weight for the highest number of possible disulfide bridges and if there is a single cysteine left then this one should be calculated with an sulfhydryl group?

This option would also be nice for the iep calculation.

"Is there a need for single cysteines to allow for inter-chain disulphide 
bridges?"
Not currently I believe that we then turn into a level where you need human interaction. 

Right now no further adjustments in my mind. 

Do you have an estimated time range when I can expect the next release?



Best Regards
Carsten P. Sönksen
Senior Scientist

Novozymes A/S
Krogshoejvej 36

2880 Bagsvaerd Denmark
Phone: +45 44461123
Mobile: +45 30771123
E-mail: caps at novozymes.com

Novozymes A/S (reg. no.: 10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark
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-----Original Message-----
From: Peter Rice [mailto:pmr at ebi.ac.uk] 
Sent: 25. august 2009 14:57
To: CAPS (Carsten P. Sönksen)
Cc: emboss at lists.open-bio.org; TAPO (Thomas Agersten Poulsen)
Subject: Re: [EMBOSS] Pepstats "Molecular weight" calculations

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