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

Jones, Mike Mike.Jones@mpi.com
Fri, 19 Apr 2002 15:42:06 -0400

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

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. 


>-----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.
>>Do You Yahoo!?
>>Yahoo! Tax Center - online filing with TurboTax
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