Twenty years of two-dimensional electrophoresis: past, present and future

Rapid mass spectrometric identification of proteins from two-dimensional polyacrylamide gels after in gel proteolytic digestion

We report a rapid method for identifying proteins resolved by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) using matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS). In-gel digestion was performed in a way such that the volume ratio of trypsin solution to gel plug was quantitatively controlled to promote reproducible digestion and to maximize the digestion yield. To make the digestion samples more compatible with MALDI-MS, the volatile salt ammonium bicarbonate in the digestion buffer was largely removed prior to peptide extraction. Samples of mixed tryptic peptides from in-gel digestion were used without purification to obtain molecular weights by MALDI-MS with alpha-cyano, 4-hydroxy-cinnamic acid as the matrix. Modifications of MALDI sample loading procedures improved the detection sensitivity by one half to one order of magnitude. The peptide mass peaks in MALDI-MS spectra were distinguished from those of impurities by using several types of controls, and masses were corrected by using trypsin autodigestion fragments as internal calibration standards. Two different peptide-matching computer programs were used to interrogate sequence databases and identify proteins. Identification was enhanced by generation of orthogonal data sets (by using different proteases) and by including experimental values of isoelectric point (pI) and molecular weight to exclude false entries in the candidate lists. Approximately 1% of the material from a spot was used in each sample loading, and nine protein spots from rat liver 2-D PAGE gels were identified correctly, as judged by comparison with identification results previously obtained from Edman sequencing. A previously identified low-abundance spot was not identified by MALDI-MS, presumably because there was insufficient material in a single gel. The sample handling procedure reported here should permit us to identify many 2-D PAGE protein spots of medium abundance.

Of genomes and proteomes

The era of complete genome sequences has arrived and with it vast amounts of data which must be annotated, cross referenced, and placed within the regulatory networks which define the physiology of an organism. One eucaryotic and three procaryotic genomes have been completed and the data made available and another 50 sequences are expected to be completed by the end of the decade. One of the first steps in the new post genome era will be to decipher the functions of the huge numbers of new open reading frames. Various approaches to investigate what unknown genes do and how genes interact together within an organism are being undertaken, including (1) the simultaneous measurement of the expression levels of all genes in a cell and (2) the mapping and quantitation of all proteins expressed within a cell. The idea of systematically mapping and identifying the total protein complement of the genome (the "proteome") arose over 20 years ago when the separation of proteins from total cell extracts by two dimensional (2D) gel electrophoresis was developed. This review will focus on the use of 2D gel electrophoresis as the basis for constructing proteome maps and on the rapid advances in mass spectrometry which will allow the large-scale, automated identification of proteins which is necessary for the creation of such databases.