Several excellent reviews are available covering all of these distinct flavors of MS-based proteomics. Additionally, it can also be used to chart proteome-wide protein–protein interactions and various post-translational modifications (PTMs). MS-based proteomics provides a means to measure proteome-wide protein abundances and monitor them upon perturbation of a system. Herein proteins are identified and quantified following enzymatic digestion into easily amenable smaller peptides, whose sequences can be determined by different fragmentation methods and matched by well-developed search algorithms against protein, RNA, and DNA databases. Focusing on proteins and peptides, to date the dominant portion of MS-based analysis is performed by peptide-centric proteomics. This diversity originates not only from the many different biomolecules that can be analyzed and investigated, such as proteins, peptides, lipids, DNA, RNA, carbohydrates, and metabolites, but also from the wide assortment of tools available to characterize them. This review focuses on recent developments, particularly in high-resolution native MS, describing applications in the structural analysis of protein assemblies, proteoform profiling of─among others─biopharmaceuticals and plasma proteins, and quantitative and qualitative analysis of protein–ligand interactions, with the latter covering lipid, drug, and carbohydrate molecules, to name a few.īiological mass spectrometry comes in many flavors. With the advent of dedicated mass analyzers, sample preparation and separation approaches, targeted fragmentation techniques, and software solutions, the number of practitioners and novel applications has risen in both academia and industry. Native MS represents a relatively recent addition to the analytical toolbox of mass spectrometry and has over the past decade experienced immense growth, especially in enhancing sensitivity and resolving power but also in ease of use. As such, native MS enables the study of secondary, tertiary, and even quaternary structure of proteins and other biomolecules. Native mass spectrometry (MS) involves the analysis and characterization of macromolecules, predominantly intact proteins and protein complexes, whereby as much as possible the native structural features of the analytes are retained.

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