Integrating chemical cross-linking with mass spectrometric analysis of peptides and proteins
The report provides an overview of chemical cross-linking and mass spectrometry as an integral capability for the exploration of proximity or distance constraints of secondary-structure building blocks in proteins, individual or in complex. The use of cross-linkers is to chemically fix spatial relationships of such building blocks, with mass spectrometry helping identify partners by correlating amino-acid-sequence patterns. Distance constraints relate to the maximum span provided by a linker, and just a few of these may suffice to confirm a protein fold. Provided that interacting and contacting interfaces of given proteins are determined, proteins can be identified even in complex milieu such as cell lysates. The wide use of this efficient strategy is supported by the progress made in mass spectrometry and is developing with established and emerging technologies. In this chapter, an emphasis is made on the types of information this capability can provide and on the basic concepts of using ‘standard’ cross-linkers which are discussed along with mass-spectrometric analysis of cross-linked products. Principles and current tendencies in the development of novel cross-linkers are addressed in the light of analytical extraction of the cross-linked species and computer-based interpretation of their mass spectra.