title: Comparative proteomics based on stable isotope labeling and affinity selection.
abstract: 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.
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA. fregnier@purdue.edu
authors.forename: Fred E
authors.initials: FE
authors.lastname: Regnier
authors.forename: Larry
authors.initials: L
authors.lastname: Riggs
authors.forename: Roujian
authors.initials: R
authors.lastname: Zhang
authors.forename: Li
authors.initials: L
authors.lastname: Xiong
authors.forename: Peiran
authors.initials: P
authors.lastname: Liu
authors.forename: Asish
authors.initials: A
authors.lastname: Chakraborty
authors.forename: Erin
authors.initials: E
authors.lastname: Seeley
authors.forename: Cathy
authors.initials: C
authors.lastname: Sioma
authors.forename: Robert A
authors.initials: RA
authors.lastname: Thompson
mesh_terms: D000818:Animals; D002417:Cattle; D002846:Chromatography, Affinity / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D007553:Isotope Labeling / Q000379:methods*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D020543:Proteome / Q000737:chemistry*; D051381:Rats
chemical_list: D011506:Proteins; D020543:Proteome