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

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 105 components with mass accuracies of 60% of the potentially expressed proteins in the organism Deinococcus radiodurans.