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

Abhishek Pratap abhishek.vit at gmail.com
Wed Nov 12 17:55:41 EST 2008

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.

Abhishek Pratap

On Tue, Nov 11, 2008 at 3:48 AM, Vered Caspi <veredcc at bgu.ac.il> 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:veredcc at bgumail.bgu.ac.il> veredcc at bgumail.bgu.ac.il
> Tel: 08-6479034 054-7915969
> Fax: 08-6472983
>  <http://bioinfo.bgu.ac.il> http://bioinfo.bgu.ac.il
> ______________________________________________________________
> _______________________________________________
> BBB mailing list
> BBB at bioinformatics.org
> 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

ISCB-Student Council


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