Reviews & Perspectives
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?Ethical Principles, Constraints, and Opportunities in Clinical Proteomics
In Brief We introduce bioethical principles and use these as operational definitions to carry out a systematic review of the literature on ethical issues in clinical proteomics. We identify 10 ethical themes across 16 studies, many of which are familiar from other fields. We therefore survey how genomics has dealt with ethical issues and regulation. We also add our own perspectives on the ethical aspects of study design and sample treatment as well as the ethical potential of preventive proteomics profiling.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.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.Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface
Proteomics and metaproteomics are important tools for studying the spatiotemporal heterogeneous ecosystem in our gut. We review strategies and their applications to gut ecology studies, such as building a dynamical model of the MLI.Organellar Maps Through Proteomic Profiling – A Conceptual Guide
Protein subcellular localization is highly regulated and critical for protein function. Spatial proteomics aims at capturing the localization dynamics of all proteins expressed in a given cell type. Among different approaches, organellar mapping through proteomic profiling stands out as the only method capable of determining the subcellular localizations of thousands of proteins in a single experiment. Importantly, it can also detect movements of proteins between subcellular compartments, providing an unbiased systems analysis tool for investigating physiological and pathological cellular processes.
