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

[Roger Moraga]

 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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