[EMBOSS] Pepstats "Molecular weight" calculations

CAPS (Carsten P. Sönksen) CAPS at novozymes.com
Tue Aug 25 11:56:34 UTC 2009

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 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)?

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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