Tonella L, Walsh BJ, Sanchez JC, Ou K, Wilkins MR, Tyler M,
Frutiger S, Gooley AA, Pescaru I, Appel RD, Yan JX, Bairoch A,
Hoogland C, Morch FS, Hughes GJ, Williams KL, Hochstrasser DF.
'98 Escherichia coli SWISS-2DPAGE database update.
Electrophoresis. 1998 Aug;19(11):1960-71. doi: 10.1002/elps.1150191114.
The combination of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE),
computer image analysis and several protein identification techniques allowed the
Escherichia coli SWISS-2DPAGE database to be established. This is part of the
ExPASy molecular biology server accessible through the WWW at the URL address
http://www.expasy.ch/ch2d/ch2d-top.html . Here we report recent progress in the
development of the E. coli SWISS-2DPAGE database. Proteins were separated with
immobilized pH gradients in the first dimension and sodium dodecyl
sulfate-polyacrylamide gel electrophoresis in the second dimension. To increase
the resolution of the separation and thus the number of identified proteins, a
variety of wide and narrow range immobilized pH gradients were used in the first
dimension. Micropreparative gels were electroblotted onto polyvinylidene
difluoride membranes and spots were visualized by amido black staining. Protein
identification techniques such as amino acid composition analysis, gel comparison
and microsequencing were used, as well as a recently described Edman "sequence
tag" approach. Some of the above identification techniques were coupled with
database searching tools. Currently 231 polypeptides are identified on the E.
coli SWISS-2DPAGE map: 64 have been identified by N-terminal microsequencing, 39
by amino acid composition, and 82 by sequence tag. Of 153 proteins putatively
identified by gel comparison, 65 have been confirmed. Many proteins have been
identified using more than one technique. Faster progress in the E. coli proteome
project will now be possible with advances in biochemical methodology and with
the completion of the entire E. coli genome.
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