Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that does not rely on ion isolation to correlate the precursor and fragment ions. On a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), 2D MS instead uses the modulation of precursor ion radii inside the ICR cell before fragmentation and yields 2D mass spectra that show the fragmentation patterns of all the analytes. In this study, we perform 2D MS for the first time with quadrupolar detection in a dynamically harmonized ICR cell. We discuss the advantages of quadrupolar detection in 2D MS and how we adapted existing data processing techniques for accurate frequency-to-mass conversion. We apply 2D MS with quadrupolar detection to the top-down analysis of covalently labeled ubiquitin with ECD fragmentation, and we develop a workflow for label-free relative quantification of biomolecule isoforms in 2D MS.

Bruker Daltonics GmbH and Co KG Fahrenheitstraße 4 28359 Bremen Germany

Center for Chemistry and Biomedicine University of Innsbruck Innrain 80 82 6020 Innsbruck Austria

Faculty of Science Charles University Prague 12843 Czech Republic

Institut de Génétique et de Biologie Moléculaire et Cellulaire INSERM U596 CNRS UMR7104 Université de Strasbourg 1 rue Laurent Fries 67404 Illkirch Graffenstaden France

Institute of Microbiology of the Czech Academy of Sciences Prague 14220 Czech Republic

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