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: [email protected] Novozymes A/S (reg. no.: 10007127). Registered address: Krogshoejvej 36 DK-2880 Bagsvaerd, Denmark This e-mail (including any attachments) is for the intended addressee(s) only and may contain confidential and/or proprietary information protected by law. You are hereby notified that any unauthorized reading, disclosure, copying or distribution of this e-mail or use of information herein is strictly prohibited. If you are not an intended recipient you should delete this e-mail immediately. Thank you. -----Original Message----- From: Peter Rice [mailto:[email protected]] Sent: 25. august 2009 14:57 To: CAPS (Carsten P. Sönksen) Cc: [email protected]; 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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
