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* Peptide and Protein Group, European Molecular Biology Laboratory,
Meyerhofstrasse 1, Postfach 10.2209, 69012 Heidelberg, Germany; and
Communicated by Klaus Biemann, Massachusetts Institute of
Technology, Cambridge, MA, October 1, 1996
(received for review August
30, 1996)
The function of many of the uncharacterized open reading frames
discovered by genomic sequencing can be determined at the level of
expressed gene products, the proteome. However, identifying the cognate
gene from minute amounts of protein has been one of the major problems
in molecular biology. Using yeast as an example, we demonstrate here
that mass spectrometric protein identification is a general solution to
this problem given a completely sequenced genome. As a first screen,
our strategy uses automated laser desorption ionization mass
spectrometry of the peptide mixtures produced by in-gel tryptic
digestion of a protein. Up to 90% of proteins are identified by
searching sequence data bases by lists of peptide masses obtained with
high accuracy. The remaining proteins are identified by partially
sequencing several peptides of the unseparated mixture by
nanoelectrospray tandem mass spectrometry followed by data base
searching with multiple peptide sequence tags. In blind trials,
the method led to unambiguous identification in all cases. In the
largest individual protein identification project to date, a total of
150 gel spots
Proc. Natl. Acad. Sci. USA
Vol. 93,
pp. 14440-14445,
December 1996
Biochemistry
Linking genome and proteome by mass spectrometry: Large-scale
identification of yeast proteins from two dimensional gels
,, and Institut de Biochimie et Génétique Cellulaires,
Centre National de la Recherche Scientifique Unité Propre de
Recherche 9026, 1 rue Camille Saint-Saëns, 33077 Bordeaux
Cedex, France
many of them at subpicomole amountswere successfully
analyzed, greatly enlarging a yeast two-dimensional gel data base. More
than 32 proteins were novel and matched to previously uncharacterized
open reading frames in the yeast genome. This study establishes that
mass spectrometry provides the required throughput, the certainty of
identification, and the general applicability to serve as the method of
choice to connect genome and proteome.
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