Indirect study of non‐covalent protein complexes by MALDI mass spectrometry: Origins, advantages, and applications of the “intensity‐fading” approach

This review article describes the origins, advantages, and application of an indirect approach with which to study protein and other macromolecular complexes and identify the nature and site of interaction interfaces by means of conventional matrix‐assisted laser desorption ionization mass spectrometry (MALDI‐MS). First reported in 1999, it involves the detection of ion depletion or the absence of ions associated with a binding partner or domain in the MALDI mass spectrum of a mixture of interacting components compared to that for an untreated control. Later referred to as intensity‐fading in some applications, the method offers numerous advantages over the direct detection of protein and other macromolecule complexes by MALDI‐MS and even electrospray ionization (ESI) MS. The origins of this indirect method, its development for use with gel‐separated components, validation using companion biochemical assays, and application to a range of protein‐antibody and protein–drug complexes are reviewed together with software specifically developed to aid with data interpretation. The sensitivity of the approach for revealing how subtle differences in the structure of the binding partners can be detected by MALDI‐MS is also demonstrated. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:559–573, 2016