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

[Roger Moraga]

 The Protease problem was fixed. Now I can just create
them all and use them as needed, thanks.

 And the MassCalc seems to get the right results now.
Only thing is that in theory, the mass of an H and of
an H+ are slightly different, but the loss of
precision is at the fourth decimal point. Not sure if
it's very important. Also, I think at some point
MH_PLUS should be changed from a boolean, since
there're three theoretical states one could ask for,
MH+, M and M - H+ (which should add one H+ mass,
nothing, or substract one H+ mass).

 Roger.


--- "Jones, Mike" <Mike.Jones@mpi.com> wrote:
> I believe I fixed the MassCalc problem. Please let
> me know if I am still
> missing something. I think I need to add in a lot
> more features (Better
> PTM's - and Terminal modifications) now that I know
> people are using
> this. 
> 
> I was unable to reproduce the error with the
> proteases not changing.
> However, I was a little static variable happy in the
> Protease class.
> This didn't cause a problem in my test code but
> could have been in
> yours. I have removed statics were they were not
> appropriate. Let me
> know if that helps. 
> 
> Mike
> 
> >-----Original Message-----
> >From: Jones, Mike 
> >Sent: Friday, April 19, 2002 11:21 AM
> >To: Roger Moraga; biojava-l@biojava.org
> >Subject: RE: [Biojava-l] org.biojava.bio.proteomics
> >
> >
> >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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