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The higher-order structure of macromolecules is linked to their biological function. Comprehending the relationships between the body's proteins, as well as how they change, is essential to understanding disease. Proteins interact with other proteins and molecules according to how they function in biology. For example, highly specific and dynamic associations of cognate binding partners and modular protein domains govern cell growth, differentiation, and intercellular communication. Elucidating their structures can be challenging, however, potentially hampering efforts to understand their function and modulation.

Obtaining high-resolution structures of large complexes by methods such as NMR spectroscopy, X-ray crystallography, or microscopy remains a major challenge in structural biology due to the sensitivity of the methods, problems associated with sample heterogeneity, the flexibility of protein structures, and the size of the complexes.1  As a complementary approach, mass spectrometry (MS) has emerged as an important technique to characterize protein complexes in a rapid and sensitive manner.2–4  MS of a protein complex usually involves two sets of experiments, classical proteomics MS and native MS,3  which are often performed separately due to sample complexity and technical limitations. Proteomics MS, either at the peptide level (bottom-up) or at the intact protein level (top-down),5  allows for the identification of individual protein components in the protein complex. Native MS studies the higher levels of protein organization, intact protein complexes, and provides structural information such as stoichiometry and spatial information on subunit arrangements that complements conventional techniques for structural biology. Although native MS can be considered a bridge between proteomics and structural biology, further developments in areas including instrumentation, experimental processes, and software are needed to fulfill its potential.3  In-depth understanding of cellular processes and pathways requires methods that not only investigate the composition and arrangements of the various assemblies of proteins, but also provide insights into their dynamics and functional regulations.

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