Dynamic range expansion applied to mass spectrometry based on data-dependent selective ion ejection in capillary liquid chromatography Fourier transform ion cyclotron resonance for enhanced proteome characterization

The characterization of cellular proteomes is important for understanding b iochemical processes ranging from cell differentiation to cancer developmen t. In one highly promising approach, whole protein extracts or fractions ar e digested (e.g., with trypsin) and injected into a packed capillary column for subsequent separation. The separated peptides are then introduced on-l ine to an electrospray ionization source of a Fourier transform ion cyclotr on resonance (FTICR) mass spectrometer for the detection of peptide accurat e mass tags that serve as biomarkers for their parent proteins. In this wor k, we report the use of data-dependent selective external ion ejection in c onjunction with FTICR and on-line capillary LC separations for the enhanced characterization of peptide mixtures and a yeast extract proteome. The num ber of peptides identified in an LC-FTICR analysis of a yeast proteome dige st employing data-dependent rf-only dipolar ejection of the most abundant i on species prior to ion accumulation was 40% higher than that detected in a separate LC-FTICR analysis using conventional nonselective ion accumulatio n.