PNNL

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 polypeptide "accurate mass tags" (AMTs) produced by a global protein enzymatic digestion. The two stage strategy exploits Fourier transform ion cyclotron resonance mass spectrometry (FTICR) to first validate polypeptide AMTs for a specific organism, tissue or cell type from "potential mass tags" identified using conventional tandem mass spectrometry (MS/MS) methods, providing the basis for subsequent measurements without the need for MS/MS. A single high resolution capillary liquid chromatography separation combined with high sensitivity, high resolution and accurate FTICR measurements is shown to be capable of characterizing polypeptide mixtures of significantly more than 105 components with mass accuracies of