Proteomics最新文献

{"title":"Expanding the Reach of Membrane Protein-Ligand Interaction Studies Through the Integration of Mass Spectrometry and Membrane Mimetics.","authors":"Jonathon C Lambos, Ashim Bhattacharya, Mohammed Al-Seragi, Franck Duong van Hoa","doi":"10.1002/pmic.70057","DOIUrl":"https://doi.org/10.1002/pmic.70057","url":null,"abstract":"<p><p>Mass spectrometry (MS) offers robust, label-free approaches for characterizing ligand-protein interactions through two main strategies: affinity-based and stability-based assays. However, their application to membrane proteins (MPs)-a major class of drug targets-has been limited by challenges such as structural complexity, low native expression, incomplete trypsin digestion, and poor compatibility with detergent-based MS protocols. Recent progress has advanced the field along two complementary fronts. First, innovations in MS methodology, including native MS, nativeomics, solution-phase thermochemistry, and ion mobility-mass spectrometry (IM-MS), have improved the ability to preserve intact assemblies, capture co-bound lipids and ligands, and resolve conformational and energetic landscapes of MPs. Second, advances in MP solubilization and stabilization, through tailored detergent architectures, MS-compatible detergents, and membrane mimetic (MM) systems-such as nanodiscs, peptidiscs, and styrene-maleic acid (SMA) polymers-have created more native-like environments that maintain functional conformations and ligand-binding sites, enabling integration of MPs into high-throughput MS platforms for ligand screening. This review outlines key affinity- and stability-based MS approaches for MPs and highlights how advances in MS methodology and solubilization strategies are extending their scope, positioning MS and MM as an increasingly powerful platform for high-throughput discovery of MP-ligand interactions.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70057"},"PeriodicalIF":3.9,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297924","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":"Proteomics Insights Into Lysosome Biogenesis and Maturation.","authors":"Katharina Hirn, Sofía Fajardo-Callejón, Dominic Winter","doi":"10.1002/pmic.70058","DOIUrl":"https://doi.org/10.1002/pmic.70058","url":null,"abstract":"<p><p>Lysosomes constitute the main degradative organelle of most eukaryotic cells and are capable of breaking down a wide spectrum of biomolecules, including proteins, lipids, glycans, and DNA/RNA. They play crucial roles in the regulation of cellular homeostasis, acting as metabolic signaling centers for the correlation of nutrient availability and biosynthetic processes. The lysosome's importance is highlighted by several human diseases associated with its dysfunction, including both early- and late-onset conditions, dependent on the level of functional impairment. Lysosomal biogenesis presents a multi-step process consisting of various delivery routes for its individual constituents, enabling strict activity control of the currently known ∼60 lysosomal hydrolases to prevent cellular self-digestion and proper assembly of the lysosomal membrane. In this review, we recapitulate the contribution of mass spectrometry (MS)-based proteomics to the characterization of lysosomal biogenesis in the last two decades. The enrichment and proteomic analysis of lysosomes and lysosomal proteins played an invaluable role for the investigation of lysosomes, encompassing the control of lysosomal gene expression, the characterization of sorting/trafficking processes, and the assignment of lysosomal proteins. This has resulted so far in the definition of ∼350 proteins which have been identified to be located in/at lysosomes or are of crucial importance for their function.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70058"},"PeriodicalIF":3.9,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145297912","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, Natalie Reitz, Marley Dewey, Colin L Hisey","doi":"10.1002/pmic.70056","DOIUrl":"https://doi.org/10.1002/pmic.70056","url":null,"abstract":"<p><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":" ","pages":"e70056"},"PeriodicalIF":3.9,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative Proteomic Profiling of Human Cell Lines Using Capillary and Micro-Pillar Array Columns.","authors":"Christina B Schroeter, Joao A Paulo","doi":"10.1002/pmic.70052","DOIUrl":"https://doi.org/10.1002/pmic.70052","url":null,"abstract":"<p><p>Chromatographic column selection can impact proteomic profiling, yet comparative studies remain limited. Here, we evaluate the performance of a conventional flame-pulled Accucore packed-bed capillary column and a microfabricated pillar array column (µPAC) in a sample multiplexed global proteome profiling experiment using six human cell lines prepared in triplicate as a TMTpro18-plex. Overall, both chromatography columns exhibited comparable performance. Specifically, the number and overlap of quantified peptides, as well as proteins, was similar between columns. Principal component and hierarchical clustering analyses highlighted reproducible cell line-driven patterns, while correlation analyses showed high replicate consistency across column formats. Similarly, analytical parameters like XCorr scores, signal-to-noise ratio, and peak resolution showed consistency. These findings demonstrate the potential for using robust, standardized microfluidic columns, such as µPAC, in lieu of traditional pull-tipped capillary columns without sacrificing depth or quantitative accuracy. Key advantages of µPAC include its ease of use and durability in a uniform format, although this advantage does come at a higher cost. This comparative analysis offers valuable insights into column selection for TMT-based quantitative proteomics. SUMMARY: We compare a conventional flame-pulled Accucore resin-packed capillary column and a microfabricated pillar array column (µPAC)-in the context of a TMTpro18-plex experiment using six diverse human cell lines. We evaluate peptide and protein quantification, analytical performance, and reproducibility of both column formats. We demonstrate comparable performance between the two columns and highlight the potential of the robust and standardized µPAC as a viable alternative to traditional capillary columns. These findings offer insights for optimizing column selection in isobaric tag-based proteomic workflows, balancing depth, precision, ease of use, and cost. We provide researchers with evidence-based guidance to enhance experimental design and advance proteomic profiling.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70052"},"PeriodicalIF":3.9,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145237516","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":"Differential Proteomics of Large Extracellular Vesicles in Ovarian Cancer.","authors":"Kazuhiro Suzuki, Yusuke Yamamoto, Masami Kitagawa, Eri Asano-Inami, Kosuke Yoshida, Hiroaki Kajiyama, Akira Yokoi","doi":"10.1002/pmic.70054","DOIUrl":"https://doi.org/10.1002/pmic.70054","url":null,"abstract":"<p><p>Diverse extracellular vesicles (EVs) are present in all body fluids; however, knowledge of large EVs (lEVs) remains limited. Molecular EV profiles vary depending on EV size and the physiological circulatory system, even within the same patient. In this study, we aimed to characterize the proteomic profile of IEVs in ovarian cancer patients and identify lEV-protein biomarkers. We collected tissue, serum, and ascites from patients with high-grade serous ovarian cancer and concurrently separated small EVs (sEVs) and lEVs through sequential multistep centrifugation. Proteomic analysis of tissues and EVs revealed distinct EV profiles in serum and ascites, identifying 11 lEV-specific proteins in serum and 14 in ascites that were absent in sEV. Of these, seven serum-specific and 10 ascites-specific proteins were further analyzed using transcriptomic databases, revealing candidate diagnostic and prognostic lEV-protein biomarkers. Our findings underscore the importance of size-based EV separation, as particle size influences biosynthetic mechanisms, in identifying lEV-specific proteins with potential diagnostic and prognostic values. SUMMARY: This study underscores the importance of distinguishing extracellular vesicle (EV) subtypes and considering body fluid specificity in biomarker discovery. By isolating EVs based on size and stepwise separation and analyzing their proteomic profiles in ovarian cancer, we identified potential large EV (lEV)-specific biomarkers that reflect disease pathology. These findings provide a foundation for lEV-protein-based liquid biopsy approaches that could enhance the accuracy of early detection and patient stratification. Further validation in clinical settings may pave the way for more precise and personalized ovarian cancer diagnostics.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70054"},"PeriodicalIF":3.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145211253","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":"Issue Information: Proteomics 19'25","authors":"","doi":"10.1002/pmic.70053","DOIUrl":"https://doi.org/10.1002/pmic.70053","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 19","pages":"1-5"},"PeriodicalIF":3.9,"publicationDate":"2025-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70053","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145204800","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":"Oncogenic H-Ras Reprograms Madin-Darby Canine Kidney (MDCK) Cell-Derived Midbody Remnant Proteome Following Epithelial-Mesenchymal Transition.","authors":"Adnan Shafiq, Alin Rai, Rong Xu, Maoshan Chen, Wittaya Suwakulsiri, David W Greening, Richard J Simpson","doi":"10.1002/pmic.70051","DOIUrl":"https://doi.org/10.1002/pmic.70051","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Epithelial-mesenchymal transition (EMT) is a fundamental, dynamic cellular process involved in embryonic development, metastasis, organ fibrosis, and tissue regeneration. To define the molecular landscape of secreted midbody remnants (MBRs) to the EMT process, a proteome analysis of MBRs released from Madin-Darby canine kidney (MDCK) cells and following oncogenic H-Ras transformation (21D1 cells) was performed. MBRs, a new class of membranous extracellular vesicle (EV) molecularly distinct from exosomes/small EVs, were purified using sequential centrifugation/buoyant density gradient centrifugation. Proteomic profiling revealed MDCK cell-MBRs reflect their epithelial origin (e.g., enriched CDH1, DSP, THBS1, OLCN, EPCAM proteins) and 21D1 cell-MBRs their oncogenic and mesenchymal phenotype (e.g., HRAS, VIM, MMP14, CDH2, WNT5A, and enriched invasive and cell motility protein networks). Validation of proteome cargo revealed key protein networks associated with the EMT process in MBRs, and conserved MBR proteome across different cell types. Prominent findings were the unique expression of the immune checkpoint protein NT5E/CD73 (ecto-5'-nucleotidase) and ser/thr kinases LIMK1/K2 in MBRs from mesenchymal cells following their oncogenic transformation, and enrichment in Wnt signaling network proteins. These data identify the core proteome of MBRs regulated during the dynamic process of EMT and cell transformation over other EV types in context of the EMT process. SUMMARY: Epithelial-to-mesenchymal transition (EMT) is a critical cell biological process that occurs during embryonic development and cancer progression. Our study describes sequential purification of secreted midbody remnants (MBRs) and exosomes/sEVs from the in vitro cell line EMT model Madin-Darby canine kidney (MDCK) cells and MDCK cells transformed with oncogenic H-Ras (21D1 cells): Proteomics identified the repertoire of enriched MDCK-MBR proteins following EMT. MBRs display a proteome profile distinct from sEVs that is enriched with factors of the centralspindlin complex (KIF23.1, KIF4A, INCENP, CEP55, PLK1) and further includes components of the mitochondrial network, cytokinesis, microtubule movement, and intercellular connection. In the context of EMT, our data reveal enriched EMT pathways in MBRs including signaling receptor binding, regulation of cell differentiation, and Wnt, VEGF, and PDGF signaling. We have validated these findings in the context of Wnt signaling in other EV types. We identify several mesenchymal-enriched networks in MBRs associated with focal adhesion, cell matrix, kinase activity, and cell shape/organization, while epithelial-derived MBRs show enriched networks predominantly associated with mitochondrial (processing/transport), midbody, and plasma membrane annotation. Our study sheds light on the proteome architecture of MBRs following oncogenic H-Ras-induced EMT in cell transformation: collectively, our data informs ongoing efforts to delineate oncogen","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70051"},"PeriodicalIF":3.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197727","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":"Chemoproteomic Profiling of Reactive Cysteines in Response to Oxidative Stress Induced by 6-Hydroxydopamine.","authors":"Rayan Murtada, Chiho Kim, Xu-Dong Wang, Youkai Yang, Yonghao Yu","doi":"10.1002/pmic.70050","DOIUrl":"10.1002/pmic.70050","url":null,"abstract":"<p><p>Although oxidative stress is a well-established driver of neurodegeneration, it remains poorly understood as to how the global cysteine (Cys) proteome is remodeled under oxidative stress conditions. Proteins with aberrantly modified cysteines in response to oxidative stress can induce and exacerbate neurodegeneration, contributing to disorders like Alzheimer's, Parkinson's, frontotemporal dementia, and amyotrophic lateral sclerosis. In this study, we induced oxidative stress in SH-SY5Y neuronal cells by subjecting them to the neurotoxin 6-hydroxydopamine (6-OHDA). To identify proteins with altered cysteine oxidation or PTM status, we used a desthiobiotin iodoacetamide (DBIA) probe, which selectively labels cysteines with unmodified and preserved thiols. Using these unbiased chemoproteomic strategies, we identified proteins with reduced Cys reactivity to DBIA in response to 6-OHDA-induced oxidative stress. Many of these proteins are critically involved in biological processes linked to cell stress responses (e.g., mitochondrial oxidative stress and apoptosis). Furthermore, we found that two key Cys on UCHL1 (a deubiquitinase critically involved in neurodegeneration) exhibited enhanced reactivity under oxidative stress conditions. Our study defines the remodeling of the Cys proteome under 6-OHDA-induced oxidative stress conditions. Furthermore, these findings suggest potential cysteine-mediated regulatory mechanisms in response to oxidative stress, providing a valuable resource for further exploration of cysteine modifications in the context of neurodegenerative signaling.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":" ","pages":"e70050"},"PeriodicalIF":3.9,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12522117/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147155","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":"Issue Information: Proteomics 17–18'25","authors":"","doi":"10.1002/pmic.70039","DOIUrl":"10.1002/pmic.70039","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 17-18","pages":"1-5"},"PeriodicalIF":3.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.70039","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135496","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":"Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment","authors":"Gaute Hovde Bø,&nbsp;Rolf Simon Härmä,&nbsp;Claus Klingenberg,&nbsp;Veronika Kuchařová Pettersen","doi":"10.1002/pmic.70047","DOIUrl":"10.1002/pmic.70047","url":null,"abstract":"<div>\u0000 \u0000 <p><b>The following article for this Special Issue was published in an earlier Issue</b>.</p>\u0000 <p>G. H. Bø, R. S. Härmä, C. Klingenberg, V. Kuchařová Pettersen, (2025). Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment. <i>Proteomics</i>. 25, e202400150, https://doi.org/10.1002/pmic.202400150. https://onlinelibrary.wiley.com/doi/10.1002/pmic.202400150</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 17-18","pages":""},"PeriodicalIF":3.9,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145135495","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}