New separation tools for comprehensive studies of protein expression by mass spectrometry

Mass spectrometry has emerged as a core technique for protein identificatio n and characterization because of its high sensitivity, accuracy, and speed of analysis. The most widespread strategy for studying global protein expr ession in biological systems employs analytical two-dimensional polyacrylam ide gel electrophoresis (2D PAGE) followed by enzymatic degradation of isol ated protein spots, peptide mapping, and bioinformatics searches. Using thi s method, thousands of proteins can be resolved in a gel and their expressi on quantified. However certain types of proteins possessing important cellu lar functions are not easily analyzed using this strategy. These proteins i nclude membrane, low copy number; highly basic, and very large (>150 kDa) a nd small (<10 kDa) proteins. To meet the growing need to simultaneously mon itor all types of proteins in a biological system, new separation strategie s have emerged that are amenable to hyphenation to mass spectrometric techn iques. This article will review these new techniques and examine their usef ulness in studies of protein expression. (C) 2000 John Wiley & Sons, Inc.