Proteomics最新文献

{"title":"Issue Information: Proteomics 6'26","authors":"","doi":"10.1002/pmic.70141","DOIUrl":"https://doi.org/10.1002/pmic.70141","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 6","pages":"1-5"},"PeriodicalIF":3.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70141","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148095522","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"See the Unseen: Rapid, Multiparametric Single-Particle Analysis of Extracellular Vesicles With Nano-Flow Cytometry","authors":"Yunyun Hu,&nbsp;Qiujin Wu,&nbsp;Junyan Chen,&nbsp;Xin Chen,&nbsp;Haonan Di,&nbsp;Xiaomei Yan","doi":"10.1002/pmic.70078","DOIUrl":"10.1002/pmic.70078","url":null,"abstract":"<div>\u0000 \u0000 <p>Extracellular vesicles (EVs) are heterogeneous lipid membrane-bound nanoparticles that carry diverse biomolecular cargos, including proteins, nucleic acids, lipids, and metabolites. Serving as fundamental mediators of intercellular communication in both physiological and pathological contexts, EVs have become a central focus in basic and translational research. Their participation in diverse biological processes—from immune regulation and tissue homeostasis to cancer progression and neurodegenerative diseases—highlights their dual functional roles. However, the intrinsic heterogeneity of EVs poses significant challenges for accurate characterization using conventional ensemble-averaging methods. Nano-flow cytometry (nFCM) represents a transformative technological advancement for single-particle EV analysis, offering high sensitivity, throughput, and multiparametric detection capabilities. This review first examines recent progress in nFCM instrumentation that improves sensitivity and resolution. We then summarize key applications of nFCM in uncovering previously inaccessible biophysical and biochemical characteristics of EVs at the single-particle level. Finally, we discuss current limitations hindering broader implementation and outline future directions to advance the field.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 6","pages":"38-51"},"PeriodicalIF":3.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145487299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revealing the Heterogeneity of Extracellular Vesicles: From Population to Single Particle Level","authors":"Aixiang Bu,&nbsp;Guangyao Wu,&nbsp;Lianghai Hu","doi":"10.1002/pmic.70024","DOIUrl":"10.1002/pmic.70024","url":null,"abstract":"<div>\u0000 \u0000 <p>Extracellular vesicles (EVs) are secreted by cells and enclosed within lipid bilayers. These vesicles contain diverse biomolecular components, including proteins, nucleic acids, lipids, and metabolites. They serve critical roles in intercellular communication and regulate multiple physiological and pathological processes, such as immune modulation, angiogenesis, and tumorigenesis and metastasis. Notably, EVs exhibit marked heterogeneity in both physical characteristics and biomolecular composition. This article will systematically characterize the multidimensional heterogeneity of EVs at the population level through comprehensive analysis of their biogenesis origins, size distribution, surface protein, surface glycan chains, and surface lipid. Conventional population-level analyzes yield averaged molecular profiles that obscure subtype-specific functional correlations, thereby limiting mechanistic insights into EV subpopulation biology. To further understand EV heterogeneity, it is necessary to enhance our understanding about molecular characteristics of EVs from the population to the single particle level. Current single EVs analysis techniques mainly include super-resolution microscopy (SRM), atomic force microscopy (AFM), nanoparticle tracking Analysis (NTA), flow cytometry (FCM), surface enhanced Raman spectroscopy (SERS), mass spectrometry (MS), and proximity barcoding assay (PBA). In this review, we systematically examine population-level EV heterogeneity; evaluate single-particle detection methodologies; and discuss emerging technologies (e.g., click chemistry, Olink proteomics, and molecular imprinting) for resolving single EV heterogeneity.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 6","pages":"22-37"},"PeriodicalIF":3.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144783118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Migrasomes, Matrix-Bound Nanovesicles, and More: Messengers in the Matrix","authors":"Anna V. Kolesov,&nbsp;Natalie Reitz,&nbsp;Marley Dewey,&nbsp;Colin L. Hisey","doi":"10.1002/pmic.70056","DOIUrl":"10.1002/pmic.70056","url":null,"abstract":"<p>Extracellular vesicles (EVs) and particles (EPs) are diverse micro- and nanoparticles that circulate in bodily fluids and can attach to, or be deposited onto, the extracellular matrix (ECM) and other surfaces. To date, the nomenclature and classification of matrix-bound or matrix-associated EVs and EPs (MEVPs) have been unclear, largely due to a lack of consensus guidelines and a relatively miniscule amount of received attention in comparison to EVs found in fluids. Recently, there has been a growing appreciation for several subtypes of MEVPs and their roles in applications ranging from wound healing to metastasis. However, progress in these fields has largely been achieved in silos, with minimal consideration for overlap or complementary function between different MEVPs. In this article, we briefly describe this growing field with a focus on several MEVP subtypes and the lack of consensus, then discuss challenges and opportunities in improving MEVP isolation and characterization. Importantly, proteomic analyses of these unique MEVPs will be crucial in promoting rigor, reproducibility, and understanding in this exciting new field.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 6","pages":"9-21"},"PeriodicalIF":3.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13063835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of Microfluidic Geometry for Extracellular Vesicle Capture Using an Automated Parallel Pattern Search","authors":"Arvin Lim,&nbsp;A. J. Tyler,&nbsp;Isha Nayyar,&nbsp;Larry W. Chamley,&nbsp;Cherie Blenkiron,&nbsp;Colin L. Hisey,&nbsp;Richard J. Clarke","doi":"10.1002/pmic.70115","DOIUrl":"10.1002/pmic.70115","url":null,"abstract":"<p>Microfluidic affinity-based capture of extracellular vesicles (EVs) holds great promise for disease diagnostics and monitoring therapeutic EV production. However, optimizing microfluidic channel geometries for efficient EV capture remains understudied due to the effort required to experimentally test numerous designs. To overcome this, we developed an automated parallel pattern search (PPS) optimizer integrating Python, COMSOL Multiphysics, and high-performance computing. We applied this approach to optimize triangular micropillar array geometries by parameterizing periodic unit cells and maximizing simulated particle capture efficiency. Surprisingly, the highest EV capture was not achieved by maximizing the number of pillars and surface area. Instead, designs with slightly larger, more widely spaced pillars promoted EV contact by enabling slower particles to follow the contours of the pillars more closely. We validated these findings experimentally using bioreactor-produced EVs and microchannels functionalized with anti-CD63 antibodies. EVs captured in the best and worst designs were quantified using fluorescence plate reading and eluted for nanoparticle tracking analysis (NTA), confirming a significant increase in capture efficiency with the optimized design. These results highlight the power of automated microfluidic optimization to advance EV isolation technologies and demonstrate a practical strategy for improving device performance in this rapidly growing field.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 6","pages":"52-58"},"PeriodicalIF":3.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147462474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single Extracellular Vesicles and Omics","authors":"David W. Greening,&nbsp;Yanling Cai,&nbsp;Ying Zhang","doi":"10.1002/pmic.70119","DOIUrl":"10.1002/pmic.70119","url":null,"abstract":"<div>\u0000 \u0000 <p>Extracellular vesicles (EVs) are fundamental intercellular signaling organelles; these lipid-bilayer-enclosed particles are secreted by all cell types and carry a cargo of proteins, lipids, and nucleic acids to facilitate such cell communication and transfer. Advances in the field of single EV analyses, including profiling techniques, capture and detection strategies, digital technologies, multiplexing capability, machine learning, and resolution of molecular analysis have led new insights into EV biology, crucial for detecting subtle variations and rare EV populations, determine the origin and molecular features of EVs, and the absolute quantification of biomarker expression levels. This issue focuses on how single EV analysis through omics and imaging technology is advancing the characterization and refinement of EVs. These studies highlight how single-EV approaches reveal multimodal distributions, challenging assumptions of discrete EV classes toward often shared physical and molecular properties (including markers across EV types) and extending this toward other EV types, refining technology pipelines, and integrated analytical strategies.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 6","pages":"6-8"},"PeriodicalIF":3.9,"publicationDate":"2026-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70119","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147490213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"1-5"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148119289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identifying Subcellular Structure Components in Escherichia Coli by Crosslinking and SEC-MS","authors":"Rachel A. Victor,&nbsp;Austin Lipinski,&nbsp;Paul R. Langlais,&nbsp;Jacob C. Schwartz","doi":"10.1002/pmic.70105","DOIUrl":"10.1002/pmic.70105","url":null,"abstract":"<p>Cells are comprised of a broad spectrum of structures that compartmentalize biochemical and signaling mechanisms. These structures can be comprised of many biomolecules, but especially lipids, proteins, and nucleic acids. Techniques are limited to quantify or discover new subcellular structures. We explored whether a proteomics approach using chemical crosslinking followed by size-exclusion chromatography and mass spectrometry (SEC-MS) of whole cell lysates can address this challenge. Formaldehyde crosslinking was used to preserve the weak molecular interactions responsible for many protein and nucleic acid assemblies. In this study, we perform the first formaldehyde crosslinking-assisted SEC-MS in a bacterial system. We demonstrate that when expressed ectopically in <i>E. coli</i>, large structures of a known assembly protein, FUS, can be detected through SEC-MS. We then show that <i>E. coli</i> proteins are enriched in particles of large or medium size due to formaldehyde crosslinking, which is the first analysis by formaldehyde and SEC-MS for a bacterial system. Last, analysis identified previously characterized <i>E. coli</i> protein assemblies and condensates, as well as potentially novel associations of prokaryote metabolism with large subcellular bodies. We propose this unbiased method can be used to stimulate or supplement targeted methods for discovery of new cellular bodies in a wide range of cell types.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"27-36"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146016737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reduction in Synaptic Vesicle Protein Abundance but Increased Amounts of Nsg2 and Lpcat1 in Cerebral Cortices Without the Endosomal SNARE Proteins Vti1a and Vti1b","authors":"Julia Gottschalk,&nbsp;Katharina Kotschnew,&nbsp;Julia Hahn,&nbsp;Thomas Patschkowski,&nbsp;Gabriele von Fischer von Mollard","doi":"10.1002/pmic.70117","DOIUrl":"10.1002/pmic.70117","url":null,"abstract":"&lt;div&gt;\u0000 \u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;p&gt;Absence of the endosomal SNAREs vti1a and vti1b results in perinatal death and severe neuronal phenotypes in mice, while lack of one of these proteins results in minor phenotypes. Proteomic differences were investigated to obtain a deeper insight into processes in which vti1a and vti1b are involved. Here we applied a bottom-up shotgun proteomic approach to investigate the differences in wild-type, double heterozygous (DHET), vti1a&lt;i&gt;&lt;sup&gt;−/−&lt;/sup&gt;&lt;/i&gt; vti1b&lt;i&gt;&lt;sup&gt;−/−&lt;/sup&gt;&lt;/i&gt; double knockout (DKO), vti1a&lt;i&gt;&lt;sup&gt;−/−&lt;/sup&gt;&lt;/i&gt; knockout and vti1b&lt;i&gt;&lt;sup&gt;−/−&lt;/sup&gt;&lt;/i&gt; knockout cerebral cortices. Single deletions did not affect protein levels significantly. A total of 1725 proteins were detected of which 69 were less abundant and 191 proteins were more abundant in DKO cortices. Many less abundant proteins belonged to cellular components and reactome pathways synapse, synaptic vesicle cycle, vesicle mediated transport, L1CAM interaction, and cholesterol biosynthesis in pathway enrichment analysis. More abundant proteins were enriched in cellular components and Kyoto Encyclopaedia of Genes and Genomes (KEGG)-pathways such as spliceosome, ribosome, carbon metabolism, and ribonucleoprotein complex. Immunoblotting validated reduced expression levels of the tested synaptic vesicle proteins as well as increased amounts of lysophosphatidylcholine acyltransferase 1 (Lpcat1) and neuron-specific gene 2 (Nsg2), which is involved in postsynaptic AMPA-receptor recycling. These data indicate that the synapse and cell adhesion were strongly affected in DKO brains.&lt;/p&gt;\u0000 &lt;/section&gt;\u0000 \u0000 &lt;section&gt;\u0000 \u0000 &lt;h3&gt; Statement of Significance of the Study&lt;/h3&gt;\u0000 \u0000 &lt;p&gt;Distinct populations of neurons and glia cells are generated and organize into layers during brain development. Neurons develop an elaborate morphology to transmit information via axons and synapses to dendrites in receiving neurons. These neurites form via several specialized pathways of vesicle secretion and endocytosis. Fusion between these membranes requires members of the SNARE protein family. Double knockouts of the endosomal SNAREs vti1a and vti1b (DKO) result in perinatal lethality in mice with massive defects in the brain. In this study we compared the proteome of DKO brain cortices with double heterozygous controls to obtain insights into the molecular alterations and affected pathways. DKO brains contained lower amounts of synaptic proteins and proteins involved in cell adhesion, membrane trafficking and cholesterol biosynthesis. Several proteins of spliceosomes, ribosomes and carbon metabolism were more abundant in DKO brains, which may be a consequence of the reduced amounts of synaptic proteins or a shift in cell populations. Lysophosphatidylcholine acyltransferase 1 (Lpcat1) and neuron-specific gene 2 (Nsg2), which is involved i","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"86-97"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147484016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"1-5"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148089941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}