[BiO BB] Analysis of mass spectrometry results using custom protein databases

Mike Marchywka marchywka at hotmail.com
Wed Nov 12 19:38:07 EST 2008


More of a question than an answer but what exactly are you doing?
Are these cleanly sliced or were they digested in an environment where they
may have been further modified? For that matter, is the organism
unusual enough to suspect unusual post-translational modifications?
etc.



> From: veredcc at bgu.ac.il
> To: bbb at bioinformatics.org
> Date: Tue, 11 Nov 2008 13:48:46 +0200
> Subject: [BiO BB] Analysis of mass spectrometry results using custom protein databases
> 
> Hello,
> 
> I received mass spec data for proteins (tryptic peptides) of a rare
> organism. Data analysis using web-based programs against standard protein
> databases did not yield results.
> 
> We would like to run the analysis against a collection of the protein
> sequences from our organism, which we have constructed in-house.
> 
> My question is whether there is a public program which can accept the
> protein sequences, "cut" them bioinformatically, and use that to identify
> the proteins analyzed in the mass sptrometry.
> 
> Vered
> 
> ______________________________________________________________
> Vered Caspi, Ph.D.
> Bioinformatics Core Facility, Head
> National Institute for Biotechnology in the Negev
> Building 39, room 214
> Ben-Gurion University of the Negev
> Beer-Sheva 84105, Israel 
> 
> Email:  veredcc at bgumail.bgu.ac.il
> Tel: 08-6479034 054-7915969
> Fax: 08-6472983
> 
>  http://bioinfo.bgu.ac.il
> ______________________________________________________________
> 
> 
> 
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