Reviews & Perspectives
Deciphering Spatial Protein–Protein Interactions in Brain Using Proximity Labeling
In Brief PL has emerged as a powerful tool to identify proteomes in distinct cell types in brain as well as proteomes and protein–protein interaction networks in structures difficult to isolate, such as the synaptic cleft, axonal projections, or astrocyte–neuron junctions. Here, we review recent advances in PL methods and their application to neurobiology.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.Chromatin Proteomics to Study Epigenetics — Challenges and Opportunities
In Brief MS-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation. Total chromatin isolated from cells can be directly analyzed using MS, further fractionated into transcriptionally active and inactive chromatin, enriched for specific compartment or regions, and potentially used for single-locus isolation. This review highlights recent advances and discusses current challenges that should be addressed to further advance the field of chromatin proteomics.Peptide-based Interaction Proteomics
Protein-protein interactions that are mediated by short linear motifs (SLiMs) in intrinsically disordered regions (IDRs) of proteins are notoriously difficult to study. Recently, pull-downs with synthetic peptides in combination with quantitative mass spectrometry emerged as a powerful screening approach. Here, we briefly highlight the relevance of SLiMs for protein-protein interactions, outline existing screening technologies, discuss unique advantages of peptide-based interaction screens, and provide practical suggestions for setting up such peptide-based screens.Developments and Applications of Functional Protein Microarrays
Functional protein microarray is a crucial tool in the study of proteins in native, unbiased, and high-throughput manner. There is a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. Functional protein microarray is also useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases, infectious diseases, and cancers. Recently, the virion display method has been applied to produce functional GPCR array for various research and pharmaceutical applications.
