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.New Views of Old Proteins: Clarifying the Enigmatic Proteome
In Brief Capturing the biology of proteins will require improved technologies to readout their composition in space and time. Developing these improved technologies presents a major opportunity for biomedical research. How might we proceed in the decades ahead?An Expanding Repertoire of Protein Acylations
In Brief In this work, we give a general overview of the 12 main protein acylations, also including novel acylations, such as benzoylation and 2-hydroxyisobutyrylation. We summarize the recent advances in protein acylation, mainly focus on their substrates, enzymes, biological functions, and novel detecting methods and related diseases, especially in cancer. We believe that the review will provide an unprecedented and comprehensive view of protein acylations and bring important reference significance for future research.Subcellular Transcriptomics and Proteomics: A Comparative Methods Review
In Brief The interior of the cell is molecularly crowded. Its compartmentalization within organelles enables the regulation of biochemical processes and allows multifunctionality of proteins and RNAs. Subcellular information can thus give insights into the function of these biomolecules. Multiple techniques to measure such information have been established, with ever-increasing throughput and sensitivity. These techniques are covered in this review, and demonstrating their application is providing valuable insights into cellular biology, such as aiding our understanding of single-cell heterogeneity and posttranslational modifications.Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years
In Brief Starting from several organ-oriented projects, HUPO in 2010 launched the Human Proteome Project to identify and characterize the protein parts list and integrate proteomics into multiomics research. Key steps were partnerships with neXtProt, PRIDE, PeptideAtlas, Human Protein Atlas, and instrument makers; global engagement of researchers; creation of ProteomeXchange; adoption of HPP Guidelines for Interpretation of MS Data and SRMAtlas for proteotypic peptides; annual metrics of finding “missing proteins” and functionally annotating proteins; and initiatives for early career scientists.Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future
In Brief Availability of proteomics data in the public domain has become the norm, as it has been the case in genomics and transcriptomics for many years. Analogously to sequencing data, there are increasing ethical issues and legal requirements related to sensitive human clinical proteomics data. We review the current state of the art and make concrete recommendations to address these issues in the proteomics field, which are summarized in four different areas.Proteomics-Based Insights Into the SARS-CoV-2–Mediated COVID-19 Pandemic: A Review of the First Year of Research
In Brief SARS-CoV-2, the betacoronavirus that caused the COVID-19 pandemic, became a major source of human disease and death in 2020. The fundamental constituents of a virus being its genome and proteome, characterizing the proteome is essential to understanding its biology. In this review article, we survey the proteomics literature from the first year of the COVID-19 pandemic, including protein–protein interaction studies, post-translational modification studies, and work using proteomics technologies to probe host response, which collectively inform efforts to ameliorate the pandemic.Decoding Post-Translational Modification Crosstalk With Proteomics
In Brief We provide an overview of current experimental and computational proteomic methods, as well as a perspective on emerging technologies to study PTM crosstalk.Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification
In Brief Probing the human plasma proteome is attractive for biomarker and drug target discovery. Recent breakthroughs in multiplex proteomics technologies enable the simultaneous and sensitive quantification of thousands of proteins in biofluids. We provide a comprehensive guide to the methodologies, performance, advantages, and disadvantages of established and emerging technologies for the multiplexed ultrasensitive measurement of proteins. Gaining knowledge on these innovations is crucial for choosing the right multiplexed proteomics tool to critically complement traditional proteomics methods.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.A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics
In Brief Interest in mass spectrometry–based glycoproteomics analysis is increasing because of recent advances in instrumentation and data analysis tools. Such studies can provide a wealth of information across a wide spectrum of glycan classes and biological systems. However, many studies require the choice of an enrichment strategy for glycosylated species prior to analysis to obtain the maximum amount of analytical information. Here, common enrichment strategies are reviewed with strengths and weaknesses, and the practical considerations for various methods are discussed.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.
