Pharmaceutical Sciences Faculty Publications
An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements
Document Type
Article
Publication Date
5-1-2002
Journal Title
Proteomics
ISSN
1615-9853
Volume
2
Issue
5
First Page
513
Last Page
523
DOI
10.1002/1615-9861(200205)2:5<513::AID-PROT513>3.0.CO;2-W
PubMed ID
11987125
Abstract
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.
Keywords
Amino acid sequence, eubacterium, fourier analysis, isotope labeling, mass spectrometry, micrococcus, molecular weight, peptides, proteome
Recommended Citation
Smith, Richard D.; Anderson, Gordon A.; Lipton, Mary S.; Pasa-Tolic, Ljiljana; Shen, Yufeng; Conrads, Thomas P.; Veenstra, Timothy D.; and Udseth, Harold R., "An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements" (2002). Pharmaceutical Sciences Faculty Publications. 499.
https://digitalcommons.cedarville.edu/pharmaceutical_sciences_publications/499