Reviews & Perspectives
Neuroproteomics of the Synapse: Subcellular Quantification of Protein Networks and Signaling Dynamics
In Brief Advancements in MS-based proteomics have increased the study of synaptic proteins using neuroproteomics. The development of proximity, genetic labeling and bio-orthogonal amino acid labeling approaches now allow for the study of synaptic protein–protein interactions and protein signaling dynamics. In this review, we highlight studies from the last 5 years, with a focus on synapse structure, composition, functioning, or signaling and finally discuss some recent developments that could further advance the field of neuroproteomics.An Introduction to Advanced Targeted Acquisition Methods
In Brief The analytical power of targeted proteomics depends on how efficiently the mass spectrometer detects target peptides. A number of “smart” acquisition approaches have been developed that enable more targets per run and improve analytical performance such as sensitivity, specificity, and quantitative accuracy. This review provides an introduction to these methods and highlights their inherent strengths and weaknesses.Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation
In Brief Recent years have seen an explosion in novel strategies for quantitative glycomics and glycoproteomics. Whether through metabolic incorporation of stable isotopes, deposition of custom isotopic labels, or high-throughput isobaric chemical tags, these numerous novel strategies provide ease of access to glycomic and glycoproteomic investigation. This review highlights the recent innovations in labeling methods, label-free strategies, acquisition modes, and bioinformatic tools for glycan and glycopeptide quantitation, while providing critical evaluations and technical considerations to enable effective analysis.Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches
In Brief Histone post-translational modifications play essential roles in the epigenetic regulation of chromatin-related functions. Because of its high throughput, accuracy, and flexibility, mass spectrometry has emerged as a powerful tool in the epigenetic field. In this review, we describe the contributions of mass spectrometry–based proteomics in combination with distinct labeling strategies and various biological techniques to understand the roles of histone post-translational modifications and how they regulate chromatin function.Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives
In Brief In this review, we outline historical and current approaches to measure the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope–labeled amino acids. In addition, we highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigations.Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks
Interactome studies are necessary to understand cellular processes and co-elution methods are well suited for the simultaneous and global exploration of the interactome, as well as the assessment of biological perturbations of the network. These methods rely on the fundamental idea that proteins from the same complex migrate together during fractionation. We review the different separation techniques along with the quantification and bioinformatic approaches used for co-elution methods and provide design considerations to choose between them.
