U.S. flag

An official website of the United States government


Main content area

Mass spectrometry in structural proteomics: The case for radical probe protein footprinting

Downard, Kevin M., Maleknia, Simin D.
Trends in analytical chemistry 2019 v.110 pp. 293-302
amino acids, crosslinking, enzymatic treatment, hydrogen, mass spectrometry, membrane proteins, oxidation, peptide mapping, proteolysis, spectrometers, structural genomics
A critical assessment of the advantages and disadvantages of each of the solution-based structural proteomics mass spectrometry methods, known as hydrogen exchange, chemical cross-linking, limited proteolysis and radical probe protein footprinting, is presented. Separate consideration is given to each of the methodological steps involved in the chemical and enzymatic treatment of proteins and the subsequent analysis of modified or degraded proteins by mass spectrometry. A case is made to preference radical probe protein footprinting when all facets of the approaches are considered side-by-side. The RP-MS approach effects limited non-reversible oxidation at reactive amino acid side chains, the levels of which are easily resolved and measured. Furthermore, the RP-MS approach can be performed at the ion source interface with the mass spectrometer, can investigate the onset of oxidative damage, is amenable to on-plate deposition for high sample throughput, and can be applied to study otherwise intractable membrane proteins, and proteins in vivo.