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From: "Geoff Wainwright" <G.Wainwright@liverpool.ac.uk>
Date: Thu, 27 Jan 2000 23:00:03 -0000
Subject: Mass accuracy and peptide mass fingerprint results
Organization: *

Dear Group,

I wondered whether anybody could clarify a point regarding the mass accuracy
required to successfully query a database (i.e. return your sample protein
at the top of the hit list) with user-generated peptide mass fingerprint
data. I have heard that there is a limit for mass accuracy above which there
is no advantage to be gained (my own experiences also suggest this). Does
anybody have any comments, or can they point me in the direction of a
suitable publication that discusses this point?

Thanks for your time.

Geoff


Dr. G. Wainwright
School of Biological Sciences
University of Liverpool
Liverpool
L69 7ZB
United Kingdom

Tel (44)151 794 4356
FAX (44)151 794 4349

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From: David Stranz <david_stranz@MassSpec.com>
Date: Fri, 28 Jan 2000 16:27:30 -0800
Subject: Re: Mass accuracy and peptide mass fingerprint results
Organization: Sierra Analytics, LLC

Geoff -

Mass accuracy is only one factor in achieving good results in protein
database searching.  It has much greater dependence on what you
present to the database.

These criteria all play off each other:

1.  The number of peptides presented as part of a query.  (Strive for
as great a coverage as possible).
2.  The accuracy of determination of their masses.
3.  The "uniqueness" of the peptides.  (In general, higher mass
peptides are more likely to be unique).
4.  Whether MS/MS data (and thus partial sequence) is available for
one or more peptides.
5.  Other constraints (protein MW, pI, species, etc.)

but most important, if your protein isn't in the database, it will
never appear at the top of the list.

In general, if you have only MS data, greater mass accuracy will aid
greatly in eliminating false positives.  Having many peptides with low
mass accuracy will succeed in pulling out the really huge proteins
from the database, simply because the likelihood of finding matching
peptides is higher the bigger the protein.

On the other hand, as Matthias Mann and others have demonstrated,
sometimes a single peptide with an MS/MS sequence tag is sufficient to
unambiguously identify a protein.

Places to look for more information on DB searching (names of DB
search programs in parentheses):

Protana's web site:  http://www.protana.com (PepSea)
Proteometrics' web site:	http://www.proteometrics.com (PROWL)
UCSF MS Lab web site:  http://prospector.ucsf.edu/ (Protein
Prospector)
Matrix Science web site: http://www.matrixscience.com (Mascot)

Fundamental papers:

"Rapid identification of proteins by peptide-mass fingerprinting", D.
J. C. Pappin, P. Horjup, and A. J. Bleasby, Current Biology 3(6) 1993
(327-332)

"Error-tolerant identification of peptides in sequence databases by
peptide sequence tags", M. Mann and M. Wilm, Anal. Chem. 66 (24), 1994
(4390-4399)

"From electrophoretically-separated protein to identification:
Strategies for sequence and mass analysis", S. D. Patterson, Anal.
Biochem. 221, 1994 (1-15)

"Identification of the components of simple protein mixtures by
high-accuracy peptide mass mapping and database searching", O. N.
Jensen,  A. V. Podtelejnikov and M. Mann,  Anal Chem 69, 1997
(4741-4750)

Regards,

David Stranz