Reviews & Perspectives
Ten Years of Extracellular Matrix Proteomics: Accomplishments, Challenges, and Future Perspectives
In Brief The extracellular matrix (ECM) is a complex assembly of hundreds of proteins forming the architectural organizer of multicellular organisms. Over the past decade, bottom-up proteomics has become the method of choice to profile the composition of the ECM. This article reviews the state of the art in ECM proteomics research and illustrates how ECM proteomics has emerged as a powerful discovery pipeline for cancer biomarkers. This review also introduces resources available to facilitate the study of the ECM using proteomics.Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine
In Brief Proteomic and genomic studies have identified new drug targets for acute myeloid leukemia (AML), leading to new therapeutic options for certain patient subpopulations. In addition, many other drugs are in advanced stages of clinical development and proteomics keeps uncovering targets of interest. Given the large number of new therapies likely to be available for AML in the near future, identification of proteomic signatures of response for each drug will be key to select the best treatment for a given patient.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?MHC Class I Immunopeptidome: Past, Present, and Future
In Brief A pioneer in studying CD8+ T-cell immunosurveillance of viruses and tumors reviews the critical contributions of MS-based studies to early, current, and future understanding of how cells generate the MHC class I immunopeptidome: the repertoire of foreign and self-peptides presented by MHC class I molecules for T-cell recognition.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.Scaling Up Single-Cell Proteomics
In Brief Single-cell proteomics will drive the next wave of single-cell biology. This requires broad adoption of existing methods, the application of rigorous quality control standards, and the continuous advancement of the technology. The advancement will be driven by numerous innovations, including highly parallelized analysis, and will increase the throughput, quantitative accuracy, and the accessibility of the single-cell proteomics.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.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.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.Are There Indeed Spliced Peptides in the Immunopeptidome?
In Brief Peptide splicing was suggested to significantly contribute ligands to the immunopeptidome. This article argues that peptide splicing is at most very rare, even if it happens at all. Considerations against peptide splicing are based on bioinformatics calculations related to the analysis of the LC-MS/MS data, and on the abundance of water in the cells, which should compete effectively with the transpeptidation reaction, needed for peptide splicing.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.MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies
In Brief Although challenges remain in leveraging MS-based HLA-II peptidomics, investigations into the interplay between disease pathologies and the presentation of HLA-II peptides to CD4+ T cells will enable the development of future immunotherapies. In this Review article, we discuss our current understanding of HLA-II peptidomics and outstanding questions in the field and how MS-based innovations will enable us to fill knowledge gaps and help improve our ability to select HLA-II-presented antigens as targets for personalized immunotherapies.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.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 Software Tools for More Generic and Precise Intact Glycopeptide Analysis
In Brief This article provides a systematic review of the most recent MS-based strategies and corresponding software tools for the analysis of intact glycopeptides, particularly intact N-glycopeptides, reported in the last decade, including the process of identifying N-glycopeptides from MS data, the existing methods of MS data acquisition and interpretation, the quality control methods, the display of results, and the software applications.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.The Role of Data-Independent Acquisition for Glycoproteomics
In Brief As a highly abundant and diverse post-translational modification, protein glycosylation is challenging to characterize in various approaches including MS. In MS-based proteomics, data-independent acquisition (DIA) has been advanced rapidly and showed outstanding analytical performances. DIA now started to be applied in different facets of glycoproteomics, including deglycosylated and intact N-linked and O-linked glycopeptides, and screening of oxonium ions. We summarized current applications of DIA in glycoproteomics and discussed its limitations and perspectives.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.Calculating Glycoprotein Similarities From Mass Spectrometric Data
In Brief To understand the roles of glycoproteins in biological processes, it is necessary to quantify the changes that occur to glycosylation at individual sites and to the whole molecule. That glycoprotein glycosylation is inherently heterogeneous means that the distribution of glycoforms at each glycosite must be quantified in order to inform calculation of molecular similarities. We review analytical and statistical methods for determining glycoprotein molecular similarities from glycoproteomics data.Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective
In Brief This review article i) assesses the utility of current glycomic, glycoproteomic, and glycogenomic methods to characterize protein glycosylation in less-well-studied eukaryotes; ii) assembles a plausible evolutionary lineage of eukaryotic glycan–protein linkages from the last eukaryotic common ancestor through protists to multicellular plants, invertebrates, and vertebrates; and iii) highlights the diversity of peripheral glycan specializations and modifications with an emphasis on available information from diverse protist kingdoms and invertebrate animals.Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review
In Brief Glycosaminoglycans (GAGs) participate in a variety of biological functions and have a multitude of medicinal properties. Due to their non template driven biosynthesis, GAGs are produced as nonuniform complex mixtures. Mass spectrometry paired with on-line separation techniques has been utilized to determine the composition of these complex mixtures. Advances in tandem mass spectrometry have also made determining sequence information such as sulfation location and C-5 epimerization possible. This review covers recent developments in the analysis of GAGs using mass spectrometry.
