Ionization techniques have been developed to aid identification of biomolecules rather than aggressively reduce the molecule to components. Two “energy deposition” processes, electron capture dissociation (ECD) [R.A. Zubarev, Electron-capture dissociation tandem mass spectrometry, Curr. Opin. Biotechnol 15 (2004), pp. 12–16] and electron-transfer dissociation (ETD) [J.J. Coon, J. Shabanowitz, D.F. Hunt and J.E. Syka, Electron transfer dissociation of peptide anions, J. Am. Soc. Mass Spectrom 16 (2005), pp. 880–882] are commonly recognized in biomolecular analysis and proteomics. Both cleave bonds adjacent to sites of electron capture and unlike other fragmentation processes, such as collision induced dissociation (CID), the cleaved bonds are not the most labile within the molecule. The cleavages observed are less dependent on the peptide sequence so cleavages between most amino acids in the peptide backbone tend to be independent of the molecule’s size. The dominant fragmentation in ECD and ETD of peptides is the formation of c and z· ions. ECD has been demonstrated to be useful for the analysis of labile post-translational modifications such as phosphorylation and O-glycosylation and for fragmentation analysis of intact proteins.

Electrospray ionization (ESI) mass spectrometry has been shown to be further aided for elucidating structural details of proteins in solution when coupled with amide hydrogen/deuterium (H/D) exchange analysis. Charge-state distributions, and the envelopes of charges ESI forms on proteins, can provide information on solution conformations of larger proteins with smaller amounts of sample not easily performed using other techniques such as near ultraviolet circular dichroism (CD) and tryptophan fluorescence (however it is typically used in conjunction with these techniques and others such as nuclear magnetic resonance). The other techniques measure the average properties of large populations of proteins in solution so an additional advantage seen with MS is its ability to provide structural details on transient or folding intermediates.