Dear Dr Vered It depends what kind of mass spec data (file formats) you have received. In order to analyze the proteins in the Mass Spec data there is a lengthy process which I will try to zip in couple of lines.
Based on the data format you might have to pick up search engine. Search Engines (X!Tandem, Myrimatch are open source programs ) which can do this for you. The search results have to statistically validated in order to be certain that identifications by these search engines are correct coz many at times they are not. I work in the Proteomics Lab at Institute for Systems Biology, Aebersold Group. We have our own in house MS/MS analysis pipeline TPP ( http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP). This software is open source and includes X!Tandem bundled in. It would be a great place for your lab to start. In case you prefer we may gladly analyze the data for you and collaborate with you on this project. Let me know what you feel. Best Abhishek Pratap On Tue, Nov 11, 2008 at 3:48 AM, Vered Caspi <[EMAIL PROTECTED]> wrote: > 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: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] > Tel: 08-6479034 054-7915969 > Fax: 08-6472983 > > <http://bioinfo.bgu.ac.il> http://bioinfo.bgu.ac.il > ______________________________________________________________ > > > > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > -- ----------------------------- Abhishek Pratap Assistant, Aebersold Lab Institute for Systems Biology, Seattle 1441 N. 34th St. Seattle, WA 98103 ph 001-(206) 732-1419 fax 001-(206) 299-6572 www.systemsbiology.org Chair RSG-Worldwide ISCB-Student Council http://iscbsc.org/rsg www.bioinfosolutions.com _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
