Agenda: Protein analysis via mass spectrometry currently relies on two general strategies: bottom-up and top-down. In the bottom-up approach, the proteins, purified or in complex mixtures, are subjected to proteolytic digestion followed by tandem MS of the resulting peptides and protein database search of the product ion spectra. Alternatively in the top-down approach, the intact protein molecular ions, individually or in mixtures, are fragmented inside the mass spectrometer without preceding proteolysis. This approach is almost exclusively limited to Fourier Transform Ion Cyclotron Resonance (FTICR) instruments due to their superior resolving power and mass accuracy. The advantage of the top-down approach is in its ability to utilize intact protein molecular ions in MSⁿ experiments and thus preserving the information not only on the intact protein sequence but also on post-translational modifications (PTMs). This talk will cover the general strategies of top-down proteomics with examples of protein identification and characterization using the LTQ FT mass spectrometer.

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