Proteomics has propelled the rapid development of mass spectrometry (MS) in the past ten years. Conversely, the advancement of MS has greatly expanded the horizon of proteomics research by allowing it to address questions never touched before. Standing out among the recent technological innovations in MS are electron capture dissociation (ECD) and electron transfer dissociation (ETD). These electron-based fragmentation methods have shown a great potential for analysis of proteolytic peptides as well as intact proteins. A promising future lies ahead for ECD- or ETD-based techniques in proteomics research, especially in studies of protein post-translational modifications and top-down analysis of intact proteins. The mechanism, instrumentation and application of ECD/ETD, along with the spectral characteristics and data analysis of peptides ECD/ETD spectra were reviewed. The current issues in ECD/ETD applications or method development, the challenges for software development, and the outlook of these techniques in future research were also discussed.