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The development and application of electron-based ion dissociation methods as a counterpart to vibrational excitation dissociation techniques has expanded the capabilities of biomolecular mass spectrometry. Electron capture dissociation and electron transfer dissociation are powerful tandem mass spectrometry tools for sequencing multiply protonated peptide and protein cations resulting from ionization under denaturing conditions. We will discuss the basics of these fragmentation methods as applied to targeted and global proteome analyses, for bottom-up techniques that analyze peptides as well as top-down techniques that interrogate intact proteins. The unique features of electron capture/transfer dissociation that differentiate it from more common fragmentation methods will be discussed, as well as the challenges faced by researchers looking to exploit these techniques for proteomics endeavors. A growing practice in the field of biomolecular mass spectrometry is combining tandem mass spectrometry approaches to increase the depth and breadth of analyses. Therefore, we will discuss efforts to develop supplemental activation workflows that combine electron-based dissociation methods with “slow heating” activation techniques. One of the value propositions of electron-based dissociation methods is the preservation of labile post-translational modifications. Therefore, we conclude this chapter by digging deeper into the characterization and localization of chemical modifications to a polypeptide chain.

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