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From: "Tin" <dtoycr@tin.it>
Date: Sat, 02 Dec 2000 13:23:53 GMT
Subject: HELP
Organization: TIN

Good day, I am a researcher and I work by mass spectrometry. In this period
i am analysing peptides obteined by tryptic digestion of proteins in by
MS/MS using an LCQ deca. I have a problem: do you know if exist a program,
on internet, that do the protein database research using peptides MS/MS
spectra that work by identity and not by omology.

Thank you very much for your help.

Simone.



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From: david_stranz@nospam.masspec.com
Date: Mon, 04 Dec 2000 12:13:38 -0800
Subject: Re: HELP
Organization: Sierra Analytics, LLC


I don't know what you mean by "identity and not by homology".  If your
protein is an unknown, you can never be guaranteed that any search has
produced a result that -is- your protein (identity) or simply shares a
lot of similarity to the peptides you chose to use for your search
(homology).  You can only convince yourself that, based on scores, #
of peptides matched, coverage or whatever, that the highest ranking
result -is- correct.

As with any library search, if the right answer isn't in the database,
ALL answers are wrong.

Anyway, there are a large number of sites that offer MS/MS based
protein database searches.  Four of them are:

SEQUEST: direct search of MS/MS spectra
http://fields.scripps.edu/sequest/index.html

Matrix Science (Mascot): peptide mass fingerprint and MS/MS tag
http://www.matrixscience.com/

UC San Francisco (Protein Prospector, etc.): peptide mass fingerprint
and MS/MS tag
http://donatello.ucsf.edu/

Proteometrics (PROWL): peptide mass fingerprint and MS/MS tag
http://www.proteometrics.com

Cheers,

David Stranz
Sierra Analytics, LLC