[BioCocoa-dev] Peptides...

[Alexander Griekspoor]

Watch out for this guy, before you know he has speeded up your code 50 
times and you're the fool in this play...  ;-)
Alex

On 20-mrt-05, at 13:13, Koen van der Drift wrote:

>
> 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.
>
>
>
*********************************************************
                     ** Alexander Griekspoor **
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               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
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                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

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