U.S. Department of Energy

Pacific Northwest National Laboratory

An accurate mass tag strategy for quantitative and high-throughput proteome measurements.

TitleAn accurate mass tag strategy for quantitative and high-throughput proteome measurements.
Publication TypeJournal Article
Year of Publication2002
AuthorsSmith RD, Anderson GA, Lipton MS, Pasa-Tolic L, Shen Y, Conrads TP, Veenstra TD, Udseth HR
KeywordsAmino Acid Sequence, Animals, Eubacterium, Fourier Analysis, Humans, Isotope Labeling, Mass Spectrometry, Micrococcus, Molecular Sequence Data, Molecular Weight, Peptides, Proteome

We describe and demonstrate a global strategy that extends the sensitivity, dynamic range, comprehensiveness, and throughput of proteomic measurements based upon the use of peptide "accurate mass tags" (AMTs) produced by global protein enzymatic digestion. The two-stage strategy exploits Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry to validate peptide AMTs for a specific organism, tissue or cell type from "potential mass tags" identified using conventional tandem mass spectrometry (MS/MS) methods, providing greater confidence in identifications as well as the basis for subsequent measurements without the need for MS/MS, and thus with greater sensitivity and increased throughput. A single high resolution capillary liquid chromatography separation combined with high sensitivity, high resolution and accurate FT-ICR measurements has been shown capable of characterizing peptide mixtures of significantly more than 10(5) components with mass accuracies of < 1 ppm, sufficient for broad protein identification using AMTs. Other attractions of the approach include the broad and relatively unbiased proteome coverage, the capability for exploiting stable isotope labeling methods to realize high precision for relative protein abundance measurements, and the projected potential for study of mammalian proteomes when combined with additional sample fractionation. Using this strategy, in our first application we have been able to identify AMTs for >60% of the potentially expressed proteins in the organism Deinococcus radiodurans.

PubMed ID11987125
Grant ListCA81654 / CA / NCI NIH HHS / United States
NS39617 / NS / NINDS NIH HHS / United States
RR12365 / RR / NCRR NIH HHS / United States
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