[Biojava-l] org.biojava.bio.proteomics

[Jones, Mike]

I will chech into this today. Thanks for the heads up. 

>-----Original Message-----
>From: Roger Moraga [mailto:bioram1976@yahoo.com] 
>Sent: Friday, April 19, 2002 7:49 AM
>To: biojava-l@biojava.org
>Subject: [Biojava-l] org.biojava.bio.proteomics
>
>
> Hello people,
>
> I've been using biojava for a few weeks now, and I've
>found a couple of problems with the proteomics tools.
>
> First, org.biojava.bio.proteomics.MassCalc gives me
>inaccurate masses for the peptides. I noticed that the
>masses given by the Expasy mass calculator were a bit
>smaller for the peptides. Looking at the code I think
>I found out why: The code adds two times the mass of
>the OH group, whereas it should be added only once for
>the C-terminal, since the N-terminal gains an H, NOT
>an OH. Additionally, if the boolean MH_PLUS is set to
>true, a third OH is added instead of an (H+).
>
> Second, I've found that if I create more than one
>protease, when trying to digest a sequence the last
>created protease will be used, regardless of which one
>was specified with digest.setProtese(). So, if I want
>to use more than one (like digest with CnBR, grab the
>fragments longer than X, digest them with trypsin), I
>have to define it just before the digest, so I have to
>store the parameters for that protease somewhere else.
>Or am I missing something?
>
> Cheers,
>
> Roger Moraga.
>
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