I would like to add one comment to the discussion of peptide mass
fingerprinting. Ken wrote in his last comment that he feels that mass
mapping is a bit oversold. I certainly agree with him in this respect. We
have seen a flood of papers (very impressive ones, I must say) which imply
that almost any protein can be identified if it is in some data base.
Whether this is achieved by mass mapping alone or by searching data banks
with CAD spectra is not being discussed here. However, I am under the
impression that the technology is stuck in the 'identification corner'.
However, how many organisms are sequenced completely? 12 or 15? I don't
know. If you think how many other organisms are not sequenced the
available sequences for identification of a given protein are SMALL!
Especially the mass spec companies are trying to sell us the idea that
once you have the proper technology and software at hand, you can identify
almost anything. Yes, that's true, but only if something is in a data
bank. Let's face it: if you are dealing with an unknown, mass spectrometry
is pretty bad to deduce a sequence (except those nice peptides which
happen to fragment very well, but our experience is against that, namely
that you can read a tiny bit of sequence, the rest is garbage). And I
think out of such inability to produce sequence data from any given
peptide came the idea to turn this into an advantage, namely to identify
proteins rather than going through dedicated structure elucidation of real
unknowns.
Don't get it wrong: we've been given extremely versatile MS methods for
protein identification. However, it is foreseeable that the sequencing
projects which produce the basis for all the identification methods will
stop at some point. And then what? Don't forget the aspect that there are
still so many unknown proteins in various organisms that I find it
personally a bit sad if such an elegant method as mass spectrometric
structure elucidation is being kept on the level of mere protein
identification.
Best regards
Paul
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Paul Jenoe, PhD
Department of Biochemistry
Biozentrum of the University of Basel
Klingelbergstrasse 70
CH-4056 Basel
Switzerland
Tel. ++41 61 267 21 68
Fax. ++41 61 267 21 48
e-mail jenoe@ubaclu.unibas.ch
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