Comparative proteomics based on stable isotope labeling and affinity selection

• Published in: Journal of mass spectrometry. Vol. 37; no. 2; pp. 133 - 145
• Main Authors: Regnier, Fred E., Riggs, Larry, Zhang, Roujian, Xiong, Li, Liu, Peiran, Chakraborty, Asish, Seeley, Erin, Sioma, Cathy, Thompson, Robert A.
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 01.02.2002; Wiley
• Subjects: Analytical, structural and metabolic biochemistry; Animals; Biological and medical sciences; Cattle; Chromatography, Affinity - methods; Computational Biology - methods; Fundamental and applied biological sciences. Psychology; General aspects, investigation methods; Humans; Isotope Labeling - methods; Protein Processing, Post-Translational; Proteins; Proteins - chemistry; Proteins - isolation & purification; Proteins - metabolism; Proteome - chemistry; Rats; Deuterium; Phosphorylation; Chemical analysis; Isotope labelling; Peptides; Oxygen 18; Carbon Isotopes; HPLC chromatography; Matrix assisted laser desorption ionization; Affinity chromatography; Carbon 13; Aminoacid sequence; Acylation; Coupled method; Glycosylation; Hydrogen Isotopes; Esterification; Protein; Peptide map; Reversed phase chromatography; Analysis method; Peptide fragment; Proteomics; Mass spectrometry; Structural analysis
• ISSN: 1076-5174; 1096-9888
• DOI: 10.1002/jms.290

Disease, external stimuli (such as drugs and toxins), and mutations cause changes in the rate of protein synthesis, post‐translational modification, inter‐compartmental transport, and degradation of proteins in living systems. Recognizing and identifying the small number of proteins involved is complicated by the complexity of biological extracts and the fact that post‐translational alterations of proteins can occur at many sites in multiple ways. It is shown here that a variety of new tools and methods based on internal standard technology are now being developed to code globally all peptides in control and experimental samples for quantification. The great advantage of these stable isotope‐labeling strategies is that mass spectrometers can rapidly target those proteins that have changed in concentration for further analysis. When coupled to stable isotope quantification, targeting can be further focused through chromatographic selection of peptide classes on the basis of specific structural features. Targeting structural features is particularly useful when they are unique to types of regulation or disease. Differential displays of targeted peptides show that stimulus‐specific markers are relatively easy to identify and will probably be diagnostically valuable tools. Copyright © 2002 John Wiley & Sons, Ltd.