I have been quite successful in identifying proteins based on peptides
maps produced from the MALDI analysis of in-gel digests. In most cases,
I use UCSF's "Protein Prospector"
(http://prospector.ucsf.edu/mshome.htm) to search databases. It offers
flexibility in terms of the database searched (eg., NCBI, Owl,
SwissProt, etc.), protease used and many other user specified
parameters. Good luck.
John J. Lennon, Ph.D.
Senior Research Scientist
Large Scale Biology Corp.
Lee, Karen wrote:
> Can anyone give any suggestions about a database search engine that
> will
> determine the identity of an unknown protein, using both masses and
> snipets of sequence from peptides generated from an enzymatic digest
> of
> that protein?
>
> Karen L. Lee
> Research Scientist
> Genzyme Corporation
> 1 Mountain Rd.
> Framingham, MA 01701-9322
> Phone: (508) 872-8400
> Fax: (508) 872-9080
> E-Mail: KLee@Genzyme.com