[BioCocoa-dev] Peptides...

Koen van der Drift kvddrift at earthlink.net
Sun Mar 20 07:13:01 EST 2005


On Mar 20, 2005, at 6:55 AM, Anastassis Perrakis wrote:

> Although all the above 100% correct the application I suggested to 
> Alex was to find a already corrected mass in the sequence. Thus the 
> charge correction is not needed, the mass is coming from 8-14 peaks 
> typically and then is corrected.
>

I guess we need to add a charge popup button, including no charge (z=0).


> What of course would be cool would be to read the scan, find the 
> peaks, get the MW and correct.
> They sell such software for 12.000 Euro - believe it or not !
> I got an Excel sheet and a little c application using GSL - they took 
> 30 mins each to make, but for both
> you need to type in the peaks.
>
> To identify peaks is trivial - I just need to get my 3-D code to 1-D 
> ;-)
> I can prototype that in c or f77 and then let Alex slow it down by a 
> factor of 50 or so ...
> Can be a fun project if I get some time.
>
> Do you guys have any MS tools for proteins already though ?
>

Not yet, I havesome code to do digesting in silico, but it is pending 
on the introduction of the BCScanner class. We had some discussions 
about this a few days ago. If you want, I can mail you (offline) my app 
that already does some of this (using a non BioCocoa class).


- Koen.




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