Top-down protein mass spectrometry can provide unique insights into protein sequence and structure, including precise proteoform identification and study of protein–ligand and protein–protein interactions. In contrast with the commonly applied bottom-up approach, top-down approaches do not include digestion of the protein of interest into small peptides, but instead rely on the ionization and subsequent fragmentation of intact proteins. As such, it is fundamentally the only way to fully characterize the composition of a proteoform. Here, we provide an overview of how a top-down protein mass spectrometry experiment is performed and point out recent applications from the literature to the reader. While some parts of the top-down workflow are broadly applicable, different research questions are best addressed with specific experimental designs. The most important divide is between studies that prioritize sequence information (i.e., proteoform identification) versus structural information (e.g., conformational studies, or mapping protein–protein or protein–ligand interactions). Another important consideration is whether to work under native or denaturing solution conditions, and the overall complexity of the sample also needs to be taken into account, as it determines whether (chromatographic) separation is required prior to MS analysis. In this review, we aim to provide enough information to support both newcomers and more experienced readers in the decision process of how to answer a potential research question most efficiently and to provide an overview of the methods that exist to answer these questions.

The use of bioactive molecules is a promising approach to enhance the bone healing properties of biomaterials. The aim of this study was to define the role of bone sialoprotein (BSP) immobilized in collagen type I in various settings. In vitro studies with human primary osteoblasts in mono- or in co-culture with endothelial cells demonstrated a slightly increased gene expression of osteogenic markers as well as an increased proliferation rate in osteoblasts after application of BSP immobilized in collagen type I. Two critical size bone defect models were used to analyze bone regeneration. BSP incorporated in collagen type I increased bone regeneration only marginally at one concentration in a calvarial defect model. To induce the mechanical stability, three-dimensional printing was used to produce a stable porous cylinder of polylactide. The cylinder was filled with collagen type I and immobilized BSP and implanted into a femoral defect of critical size in rats. This hybrid material was able to significantly induce bone regeneration. Our study clearly shows the osteogenic effect of BSP when combined with collagen type I as carrier and thereby offers various approaches and options for its use as bioactive molecule in bone substitute materials.

The DNA methyltransferase 2 (DNMT2) is an RNA modifying enzyme associated with pathophysiological processes, such as mental and metabolic disorders or cancer. Although the development of methyltransferase inhibitors remains challenging, DNMT2 is not only a promising target for drug discovery, but also for the development of activity-based probes. Here, we present covalent SAH-based DNMT2 inhibitors decorated with a new type of aryl warhead. Based on a noncovalent DNMT2 inhibitor with N-benzyl substituent, the Topliss scheme was followed for optimization. The results showed that electrondeficient benzyl moieties highly increased affinity. By decorating the structures with strong electron-withdrawing moieties and leaving groups, we adjusted the electrophilicity to create covalent DNMT2 inhibitors. A 4-bromo-3-nitrophenylsulfonamide-decorated SAH derivative (80) turned out to be the most potent (IC 50 = 1.2 ± 0.1 μM) and selective inhibitor. Protein mass spectrometry confirmed the covalent reaction with the catalytically active cysteine-79.

In recent years, top‐down mass spectrometry has become a widely used approach to study proteoforms; however, improving sequence coverage remains an important goal. Here, two different proteins, α‐synuclein and bovine carbonic anhydrase, were subjected to top‐down collision‐induced dissociation (CID) after electrospray ionisation. Two high‐boiling solvents, DMSO and propylene carbonate, were added to the protein solution in low concentration (2%) and the effects on the top‐down fragmentation patterns of the proteins were systematically investigated. Each sample was measured in triplicate, which revealed highly reproducible differences in the top‐down CID fragmentation patterns in the presence of a solution additive, even if the same precursor charge state was isolated in the quadrupole of the instrument. Further investigation supports the solution condition‐dependent selective formation of different protonation site isomers as the underlying cause of these differences. Higher sequence coverage was often observed in the presence of additives, and the benefits of this approach became even more evident when datasets from different solution conditions were combined, as increases up to 35% in cleavage coverage were obtained. Overall, this approach therefore represents a promising opportunity to increase top‐down fragmentation efficiency.