Modern strategies for protein quantification in proteome analysis: Advantages and limitations

Abstract

1

Table 1. 

I.	Introduction	287
II.	Sample Preparation	289
	A. Influence of Alkylation	289
	B. Influence of Surfactants	289
III.	MS-Based Strategies for Protein Quantification	290
	A. Isotope-Coded Affinity Tags (ICAT)	291
	B. Mass-Coded Abundance Tagging (MCAT)	293
	C. Stable Isotope-Labeling of Proteins/Peptides	294
	D. Global Internal Standard Strategy (GIST)	294
	E. Two-D Gel or Column Electrophoresis/MALDI-TOF-MS	295
	F. Fluorescence, Two-Dimensional Differential in-Gel Electrophoresis (DIGE) for Quantitative Proteomics	296
IV.	Discussion	299
V.	Concluding Remarks	300
Acknowledgments		300
References		300

Over the last 3 years, a number of mass spectrometry-based methods for the simultaneous identification and quantification of individual proteins within complex mixtures have been reported. Most, if not all, of such strategies apply a two-step approach: the first for the separation of proteins or peptides, and the second uses mass spectrometry to identify and quantify the individual components. To simplify the outcome of both steps, certain chemicals and heavy-isotope-labeling are commonly used in the early stages of sample preparation (except in differential fluorescence labeling protocols). The ultimate goal of these strategies is to be able to identify every protein expressed in a cell or tissue, and to determine each protein's abundance, state of modification, and possible involvement in multi-protein complexes. In this review, an attempt is made to highlight the salient characteristics of the existing strategies with particular attention to their strengths and weaknesses. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 21:287–302, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mas.10032