<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Progress is reviewed towards the development of a global strategy that aims to extend the
sensitivity, dynamic range, comprehensiveness and throughput of proteomic measurements
based upon the use of high performance separations and mass spectrometry. The approach
uses high accuracy mass measurements from Fourier transform ion cyclotron resonance
mass spectrometry (FTICR) to validate peptide ‘accurate mass tags’ (AMTs) produced by
global protein enzymatic digestions for a specific organism, tissue or cell type from
‘potential mass tags’ tentatively identified using conventional tandem mass spectrometry
(MS/MS). This provides the basis for subsequent measurements without the need for MS/
MS. High resolution capillary liquid chromatography separations combined with high
sensitivity, and high resolution accurate FTICR measurements are shown to be capable of
characterizing peptide mixtures of more than 10<sup>5</sup> components. The strategy has been initially demonstrated using the microorganisms 
<italic>Saccharomyces cerevisiae</italic> and <italic>Deinococcus radiodurans.</italic> Advantages of the approach include the high confidence of protein
identification, its broad proteome coverage, high sensitivity, and the capability for stableisotope
labeling methods for precise relative protein abundance measurements.</p> <p><italic>Abbreviations</italic>: LC, liquid chromatography; FTICR, Fourier transform ion cyclotron
resonance; AMT, accurate mass tag; PMT, potential mass tag; MMA, mass measurement
accuracy; MS, mass spectrometry; MS/MS, tandem mass spectrometry; ppm, parts per
million.</p>
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Comp Funct Genomics. 2002 Apr; 3(2):143-150