Abstract
| I. | Introduction | 182 |
| II. | Relative Quantitation | 184 |
| | A. 2‐D Gel Electrophoresis | 184 |
| | B. Metabolic Isotopic Labeling | 185 |
| | 1. ^15^N | 185 |
| | 2. ^13^C Enrichment and Depletion | 185 |
| | 3. Select Isotopic Amino Acid Incorporation | 186 |
| | C. Chemical Labeling | 186 |
| | 1. Labeling During Proteolysis: ^18^O Incorporation During Enzymatic Cleavage | 186 |
| | 2. Isotopic Tags—Isotope‐Codes Affinity Tag Reagents (ICAT) | 187 |
| | 3. Isotopic Tags—Acid‐Labile Isotope‐Coded Extractants (ALICE) | 188 |
| | 4. Lysine‐Specific Labeling | 189 |
| | 5. Phosphoserine‐ and Phosphothreonine‐Specific Labeling | 189 |
| | 6. N‐Terminus Labeling | 189 |
| | a. Nicotinyl‐N‐hyxroxysuccinimide | 189 |
| | b. Acylation | 189 |
| | c. Amidination‐quantitation using enhanced signal tags (QUEST) | 190 |
| | d. C‐terminusu labeling | 190 |
| | D. Differential Mass Mapping | 190 |
| III. | Absolute Quantitation | 191 |
| IV. | Choice of Instrumentation | 191 |
| V. | Overview, Discussion, and Future Directions | 191 |
| References | | 192 |
Techniques for the quantitation of proteins and peptides by mass spectrometry (MS) are reviewed. A range of labeling processes is discussed, including metabolic, enzymatic, and chemical labeling, and techniques that can be employed for comparative and absolute quantitation are presented. Advantages and drawbacks of the techniques are discussed, and suggestions for the appropriate uses of the methodologies are explained. Overall, the metabolic incorporation of isotopic labels provides the most accurate labeling strategy, and is most useful when an internal standard for comparative quantitation is needed. However, that technique is limited to research that uses cultured cells. © 2003 Wiley Periodicals, Inc., Mass Spec Rev 22:182–194, 2003; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/mas.10048