Journal of proteomics最新文献

{"title":"Mining the plasma proteome: Evaluation of enrichment methods for depth and reproducibility","authors":"K. Roger ,&nbsp;I. Metatla ,&nbsp;S. Ceccacci ,&nbsp;K. Wahbi ,&nbsp;L. Motté ,&nbsp;C. Chhuon ,&nbsp;I.C. Guerrera","doi":"10.1016/j.jprot.2025.105519","DOIUrl":"10.1016/j.jprot.2025.105519","url":null,"abstract":"<div><div>Plasma is a complex biological fluid containing extracellular vesicles (EVs), residual platelets, and soluble proteins. While conventional plasma proteomics typically identifies hundreds of proteins, recent enrichment strategies have expanded coverage to thousands. It is still unclear whether these methods enrich preferentially different classes of protein and whether they allow for reliable quantification. Here, we compared three common advanced proteomic workflows—Proteograph (Seer), Mag-Net (ReSynBio), and ENRICHplus (PreOmics) as well as EV enrichment obtained by centrifugation. We explore the content in soluble proteins, EV cargo, and platelet-derived proteins after the enrichments. Quantification was evaluated comparing each method to neat plasma using protein coefficient of variation and point-biserial correlation.</div><div>We quantified an average of ∼4500 proteins with EV centrifugation, ∼4000 with Seer, ∼2800 with ENRICHplus, ∼2300 with Mag-Net, and ∼ 900 with neat plasma. Each method enriched distinct sets of protein signatures: EV preparations were enriched with EV markers such as CD81; ENRICHplus predominantly captured lipoproteins; and Proteograph was enriched for cytokines and hormones. Platelet protein intensity was directly correlated with total protein identifications but did not compromise quantification of low-abundance proteins. Across 50 healthy individuals, Proteograph consistently demonstrated reproducible enrichment and depletion patterns, with some reported exceptions.</div><div>Our results highlight the strengths and biases of different plasma enrichment strategies.</div></div><div><h3>Significance</h3><div>This study benchmarks corona formation strategies for enriching low-abundance plasma proteins, including those from platelets and EVs. While enabling deeper proteome coverage compared to depletion methods, these approaches also reshape the intensity landscape and reveal method-specific patterns in protein class enrichment and in quantification repeatability.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105519"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144883084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteoformics: Current status and future perspectives","authors":"Zheng Fang ,&nbsp;Yanjun Zhang ,&nbsp;Xiaoxia Feng ,&nbsp;Na Li ,&nbsp;Liang Chen ,&nbsp;Xianquan Zhan","doi":"10.1016/j.jprot.2025.105524","DOIUrl":"10.1016/j.jprot.2025.105524","url":null,"abstract":"<div><div>Proteoforms represent the ultimate structural/functional forms of a gene product, defined by multiple factors, including amino acid sequences, post-translational modifications, spatial conformations, and interactions with other molecules. The human proteoform diversity significantly exceeds the number of human genes/transcripts, emphasizing the need for advanced analytical methods to characterize this complexity. Two-dimensional gel electrophoresis-liquid chromatography/mass spectrometry (2DE-LC/MS) and top-down MS (TD-MS) are complementary to detect, identify, and quantify the large-scale proteoforms. The emerging AI tools for structural biology such as AlphaFold 3 and D-I-TASSER will enable proteoformics to be high-throughput and precisely predict spatial conformations and molecular interactions. Integrating the large-scale experimental data derived from 2DE-LC/MS and TD-MS with AI-driven high-throughput structural analysis paves the way to deeply understand proteoform diversity and functionality. The combination of advanced 2DE-LC/MS, TD-MS, and AI-driven structural analysis represents a pivotal advancement in proteoformics. This integrated approach enables the comprehensive profiling of proteoforms, providing critical insights into their roles in health care. Such advancements hold promise for predictive, preventive, and personalized medicine, particularly through biomarker discovery and therapeutic target identification. Future developments in high-throughput capabilities and dynamic modeling are expected to address current challenges and further expand the applicability of proteoformics in biological and clinical research.</div></div><div><h3>Significance</h3><div>Proteoformics is the future of proteomics, whose two main complementary analytical approaches are 2DE-LC/MS and TD-MS. The AI-driven large-cale structural analysis enables to high-throughput and precisely analyze spatial conformations and molecular interactions of proteoforms, which helps to deeply understand proteoform diversity and functionality. Proteoformics holds transformative potential to uncover biomarkers, guide targeted therapies, and advance predictive diagnosis in the context of personalized medicine.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105524"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144894990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential kidney biomarkers in urinary extracellular vesicles from end stage renal disease and post-transplant patients","authors":"Maritza G. Verdugo-Molinares ,&nbsp;Marco Ku-Centurion ,&nbsp;Laura Cortes-Sanabria ,&nbsp;Yadira O. Lugo-Melchor ,&nbsp;Emilie Pinault ,&nbsp;Luis Evangelista ,&nbsp;Cesar O. Ramos-Garcia ,&nbsp;Pierre Marquet ,&nbsp;Zesergio Melo","doi":"10.1016/j.jprot.2025.105523","DOIUrl":"10.1016/j.jprot.2025.105523","url":null,"abstract":"<div><div>Chronic kidney disease is a multifactorial entity characterized by decreased glomerular filtration rate (GFR). The last stage of the disease requires renal replacement therapy or kidney transplantation. As a disease with no treatment at earlier stages, and few biomarkers available, proteomics represent an excellent tool searching for new more efficient biomarkers. Urinary extracellular vesicles are an important source of information for kidney alterations, and their collection is not invasive. In this exploratory study, we worked on urine samples collected from patients at Centro Medico Nacional de Occidente in Guadalajara, Jalisco, and isolated urinary extracellular vesicles (uEVs) by ultracentrifugation. Our objective was to compare the Proteomic Profile of uEVs between Mexican patients with normal kidney function, end-stage renal disease, or kidney transplantation. High resolution mass spectrometry analysis reveals alterations in end-stage renal disease regarding the energy metabolism, cytoskeleton organization and cell motility. Proteomic alterations in transplant patients point towards the conservation of fibrotic process. Important proteins such as cystatins can be proposed as candidates for kidney transplant monitoring, while Gelsolin, a protein with an important role in assessing podocyte damage, stands out as a probable marker of chronic kidney disease. Data are available via ProteomeXchange with identifier PXD065380.</div></div><div><h3>Significance</h3><div>Chronic Kidney disease is a growing public health burden, increasing each year, and favored by major chronic diseases such as diabetes and hypertension. Although Mexico is one of the countries with the highest incidence of chronic kidney disease, proteomics studies involving Mexican patients had not yet been conducted. uEVs are features of particular interest to study the disease and discover biomarkers. We characterized the uEVs proteomic profile in Mexican patients, providing new insights into the pathogenesis of chronic kidney disease and kidney transplantation disorders. We identified promising biomarker candidates for transplant monitoring, and one as an early indicator of ESRD progression. uEVs may serve as a non-invasive platform for renal disease investigation, potentially offering non-invasive biomarkers for patient monitoring as well as mechanistic insights for future research into kidney pathophysiology.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105523"},"PeriodicalIF":2.8,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144886149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expanding the landscape of lysine acetylation stoichiometry and clinical impact","authors":"Sergio Encarnación-Guevara ,&nbsp;Jeovanis Gil","doi":"10.1016/j.jprot.2025.105522","DOIUrl":"10.1016/j.jprot.2025.105522","url":null,"abstract":"<div><div>Lysine acetylation, once viewed primarily as a histone mark, is now recognized as a widespread regulator of protein function. Recent breakthroughs in chemical labeling, isotopic tagging workflows, and data-independent acquisition mass spectrometry enable precise, site-specific quantification of acetylation stoichiometry. This quantitative “acetylomics” approach reveals a “rheostat” model, where most acetylation sites exhibit low occupancy, acting as subtle modulators, while a subset of highly acetylated lysines (e.g., p53 C-terminus, AKT1, histones) serve as pivotal regulatory switches in gene expression, metabolism, and cell fate. Site-specific occupancy changes (e.g., p53, PKM2) increasingly serve as robust biomarkers for cancer diagnosis, prognosis, and therapeutic monitoring, often surpassing mRNA or total protein levels. Quantitative acetylation data now guide the development of targeted epigenetic therapies, including HDAC and p300/CBP inhibitors. Beyond oncology, acetylomics can pinpoint metabolic bottlenecks in heart failure, epigenetic deficits in neurodegenerative conditions, and inflammatory signaling nodes. With advances in high-throughput workflows, FFPE and liquid biopsy compatibility, and microfluidic platforms, acetylation stoichiometry is poised for clinical translation. We highlight both the promise and challenges of this emerging dimension of precision medicine, emphasizing the need for integrated multi-omics approaches and robust clinical validation to fully realize the potential of quantitative acetylomics in disease diagnosis and therapy.</div></div><div><h3>Significance</h3><div>Understanding the extent of acetylation occupancy in proteins, beyond simply determining presence or absence of acetylation, has profound implications for biology and medicine. This review emphasizes the importance of acetylation stoichiometry, connecting advanced proteomic technologies with translational science. We emphasize that quantifying site occupancy reveals which acetylation events truly modulate enzyme function. For instance, it can identify which acetylation events truly modulate enzyme activity or gene expression. Additionally, it can highlight molecular changes in diseases like cancer that are not apparent through qualitative analyses. These quantitative insights pave the way for clinical innovations, including novel biomarkers that stratify patients based on their acetylation profiles and targeted therapies that modulate acetylation levels. In summary, this work highlights the evolving landscape of protein acetylation research over the past two decades and its increasing influence on translational proteomics, celebrating milestones achieved by the global research community.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105522"},"PeriodicalIF":2.8,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144842547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global profiling of protein lysine Malonylation during goat intramuscular Preadipocyte differentiation","authors":"Changheng Yang ,&nbsp;Haiyang Li ,&nbsp;Zijun Xu ,&nbsp;Yaqiu Lin ,&nbsp;Yong Wang ,&nbsp;Lian Huang ,&nbsp;Hua Xiang ,&nbsp;Jiangjiang Zhu","doi":"10.1016/j.jprot.2025.105521","DOIUrl":"10.1016/j.jprot.2025.105521","url":null,"abstract":"<div><div>Enhancing intramuscular fat (IMF) to improve the quality of livestock product has long been a goal in animal breeding. Recent studies have revealed a strong connection between malonylation and lipid metabolism, yet the function of malonylated proteins in ruminants largely unclear. In the present study, we identified the third day of goat intramuscular preadipocyte differentiation as a critical time point for lipid accumulation, with no significant alterations in malonylation levels. We identified 212 and 216 malonylated proteins on day 0 (d0) and day 3 (d3) of differentiation, respectively, enrichment in pathways such as glycolysis/gluconeogenesis, tight junctions, and actin cytoskeleton regulation. Our findings demonstrate the consistent presence of malonylation during preadipocyte differentiation, with minor quantitative variations, and highlight key malonylated proteins closely associated with lipid metabolism, including acetyl-CoA carboxylase (ACACA), translation control tumor protein 1 (TPT1), phosphoglycerate kinase 1 (PGK1), annexin A6 (ANXA6), and annexin A2 (ANXA2). Collectively, our study uncovers critical malonylated proteins during preadipocyte differentiation, establishing a foundation for exploring their roles in intramuscular fat deposition.</div></div><div><h3>Significance</h3><div>Currently, efforts are being made to improve meat quality by enhancing intramuscular fat (IMF) deposition, thereby promoting the development of the livestock industry. This study addresses a critical gap in our understanding of malonylation, a key post-translational modification, in livestock. By constructing the first malonylation protein modification map in goats and revealing dynamic changes during intramuscular preadipocyte differentiation, this research offers novel insights into the regulatory roles of malonylation in fat deposition. The findings not only advance the field of livestock proteomics but also provide a theoretical foundation for improving meat quality and exploring metabolic regulation in animals.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105521"},"PeriodicalIF":2.8,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144855619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic and transcriptomic analyses reveal new insights into allergens in Ligustrum lucidum pollen","authors":"Juan Carlos Vizuet-de-Rueda ,&nbsp;Josaphat M. Montero-Vargas ,&nbsp;Alberto C. López-Calleja ,&nbsp;María Z.T. Manríquez-Ventura ,&nbsp;Luis M. Teran","doi":"10.1016/j.jprot.2025.105520","DOIUrl":"10.1016/j.jprot.2025.105520","url":null,"abstract":"&lt;div&gt;&lt;div&gt;Pollen aeroallergens cause up to 40 % of respiratory allergies and are challenging to control due to their widespread distribution in the environment. The pollen of &lt;em&gt;Ligustrum lucidum&lt;/em&gt; (privet) is a significant source of inhalant allergens. However, despite its clinical relevance, the protein composition of &lt;em&gt;L. lucidum&lt;/em&gt; pollen remains poorly characterized. Therefore, we employed an integrated proteomic and transcriptomic approach to explore its potential allergen composition, focusing on possible cross-reactivity with &lt;em&gt;Olea europea&lt;/em&gt; (olive), a well-studied allergenic relative. Using LC-MS/MS-based proteomics and RNA-seq transcriptomics, we detected 13 of the 15 known olive-like allergens, demonstrating high cross-species conservation. Proteomic analysis identified nine homologous allergens, including Ole e 1, Ole e 2, Ole e 3, Ole e 5, Ole e 6, Ole e 9, Ole e 12, Ole e 13, and Ole e 14. Transcriptomic analysis revealed four additional putative allergens: Ole e 8, Ole e 10, Ole e 11, and Ole e 15. These proteins shared 74–95 % sequence identity with their olive counterparts and exhibited multiple isoforms. Our findings provide a set of &lt;em&gt;L. lucidum&lt;/em&gt; pollen potential allergens and highlight the utility of multi-omics in allergen discovery. However, further clinical validation of these putative novel allergens is needed to assess their role in sensitization and cross-reactivity.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Significance&lt;/h3&gt;&lt;div&gt;Privet (&lt;em&gt;Ligustrum&lt;/em&gt;), a genus within the Oleaceae family, is biologically significant due to its role in triggering allergic respiratory diseases worldwide. As a close relative of olive (&lt;em&gt;Olea europaea&lt;/em&gt;) and ash (&lt;em&gt;Fraxinus&lt;/em&gt;), privet shares allergenic proteins that contribute to cross-reactivity among sensitized individuals. Climate change has been shown to extend their flowering period, increasing pollen exposure and exacerbating allergic symptoms. &lt;em&gt;Ligustrum&lt;/em&gt; is widely used in urban landscaping due to its rapid growth, resistance to pollution, and adaptability to diverse soil conditions, which facilitates its global spread across North America, Europe, Asia, and South America. Notably, &lt;em&gt;L. lucidum&lt;/em&gt; is a major sensitizing agent in Mexico City, where 37 % of allergic patients react to its pollen. The first identified allergen, Lig v 1, shares homology with Ole e 1 and Fra e 1. At the same time, Lig v 2 (profilin) mirrors Ole e 2, highlighting the molecular basis for cross-reactivity within the Oleaceae family. Recent proteomic studies have uncovered additional allergens, including enolase, β-1,3-glucanase, and ATP synthase subunits, further elucidating privet's allergenic potential. The absence of genomic data for &lt;em&gt;L. lucidum&lt;/em&gt; has hindered research; however, advances in transcriptomic and proteomic approaches have enabled the identification of 13 of 15 known olive-like allergens in privet pollen, paving the way for improved diagnostics and targeted therapie","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105520"},"PeriodicalIF":2.8,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144842548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Off-site processing of data-dependent and data-independent acquisition shotgun proteomics data with MASSyPupX","authors":"Jorge Noé García-Chávez ,&nbsp;Robert Winkler","doi":"10.1016/j.jprot.2025.105494","DOIUrl":"10.1016/j.jprot.2025.105494","url":null,"abstract":"<div><div>The rapid pace of shotgun proteomics data generation presents challenges for timely data analysis. In parallel, the scientific community is creating novel data interpretation tools, such as artificial intelligence, that have not yet been integrated into commercial software. Off-site data processing with free and open-source software (FOSS) enables the decentralization and scaling of informatics workflows. FOSS platforms also lower the costs of education and research. MASSyPupX is a FOSS mass spectrometry (MS) software collection that runs directly from a USB drive. Alternatively, setting up a MASSyPupX workstation or server provides a ready-to-use and reproducible MS analysis platform. Installed programming languages and libraries support the development of custom MS software and workflows. This paper demonstrates using MASSyPupX to convert and process raw shotgun proteomics data. Raw Thermo files were downloaded from ProteomeXchange and converted to the HUPO community format <span>mzML</span>. Data-dependent acquisition (DDA) data were evaluated with Comet, PeptideProphet, ProteinProphet, ProtyQuant, and the Trans-Proteomic Pipeline. Data-independent acquisition (DIA) shotgun proteomics data were analyzed with DIA-NN. Custom Bash, Python, and R scripts were used to post-process and visualize the results. The MASSyPupX project is hosted at <span><span>https://codeberg.org/LabABI/MASSyPupX</span><svg><path></path></svg></span>, and the current ISO can be downloaded from <span><span>https://doi.org/10.5281/zenodo.14618430</span><svg><path></path></svg></span>.</div><div>The MASSyPupX platform significantly advances shotgun proteomics data processing by offering a free and open-source software (FOSS) solution that is portable, scalable, and accessible. Operating directly from a USB drive or server, this Debian-based Linux distribution enables researchers to analyze data-dependent (DDA) and data- independent (DIA) acquisition proteomics data without installation, decentralizing workflows, reducing costs, and fostering collaboration and mass spectrometry data processing training. With pre-installed programming languages, libraries, and support for tools like Comet, PeptideProphet, DIA-NN, and ProtyQuant, MASSyPupX facilitates reproducible analyses, integrates cutting-edge computational techniques, and provides a user-friendly environment for education, research, and custom workflow development.</div><div>MASSyPupX democratizes access to advanced proteomics analysis, serving as a versatile tool for advancing biological and medical research through decentralized and cost-effective workflows.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105494"},"PeriodicalIF":2.8,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Q2C: A software for managing mass spectrometry facilities","authors":"Diogo B. Lima ,&nbsp;Max Ruwolt ,&nbsp;Marlon D.M. Santos ,&nbsp;Ke Pu ,&nbsp;Fan Liu ,&nbsp;Paulo C. Carvalho","doi":"10.1016/j.jprot.2025.105511","DOIUrl":"10.1016/j.jprot.2025.105511","url":null,"abstract":"<div><div>We present Q2C, an open-source software designed to streamline mass spectrometer queue management and assess performance based on quality control metrics. Q2C provides a fast and user-friendly interface to visualize projects queues, manage analysis schedules and keep track of samples that were already processed. Our software includes analytical tools to ensure equipment calibration and provides comprehensive log documentation for machine maintenance, enhancing operational efficiency and reliability. Additionally, Q2C integrates with Google™ Cloud, allowing users to access and manage the software from different locations while keeping all data synchronized and seamlessly integrated across the system. For multi-user environments, Q2C implements a write-locking mechanism that checks for concurrent operations before saving data. When conflicts are detected, subsequent write requests are automatically queued to prevent data corruption, while the interface continuously refreshes to display the most current information from the cloud storage. Finally, Q2C, a demonstration video, and a user tutorial are freely available for academic use at <span><span>https://github.com/diogobor/Q2C</span><svg><path></path></svg></span>. Data are available from the ProteomeXchange consortium (identifier PXD055186).</div></div><div><h3>Significance</h3><div>Q2C addresses a critical gap in mass spectrometry facility management by unifying sample queue management with instrument performance monitoring. It ensures optimal instrument utilization, reduces turnaround times, and enhances data quality by dynamically prioritizing and routing samples based on analysis type and urgency. Unlike existing tools, Q2C integrates queue control and QC in a single platform, maximizing operational efficiency and reliability.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105511"},"PeriodicalIF":2.8,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144768734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics reveals the role of the EamB transporter from Aeromonas hydrophila LP-2 in biofilm formation","authors":"Qiaozhen Xu ,&nbsp;Feng Tian ,&nbsp;Xinyun Wang ,&nbsp;Juanqi Lian ,&nbsp;Xiaowei Zhang ,&nbsp;Xiangmin Lin ,&nbsp;Yanling Liu","doi":"10.1016/j.jprot.2025.105510","DOIUrl":"10.1016/j.jprot.2025.105510","url":null,"abstract":"<div><div>Biofilms play a pivotal role in the survival and persistence of microorganisms, endowing them with heightened resistance to environmental stressors and antimicrobial agents. The EamB protein, which encodes an inner membrane transporter, acted as a negative regulator of biofilm formation, and the gene <em>eamB</em> deletion in the pathogen <em>Aeromonas hydrophila</em> LP-2 resulted in a significant increase in biofilm formation. Proteomic analysis revealed a total of 616 differentially abundant proteins between the <em>ΔeamB</em> and wild-type (WT) strains, with 308 downregulated and 308 upregulated. RT-qPCR was employed to verify the stability and accuracy of the proteomics data. Bioinformatic analysis indicated that EamB is involved in critical bacterial biological processes, including flagellar assembly, amino acid metabolism, and fatty acid degradation. Biofilm formation assays further revealed that supplementation with exogenous lysine significantly inhibited biofilm formation in the <em>ΔeamB</em> strain, conversely, exogenous cysteine and <em>O</em>-acetylserine obviously increased biofilm formation in the <em>ΔeamB</em> strain. These findings demonstrated that EamB may modulate bacterial biofilm formation in <em>A. hydrophila</em> through the regulation of amino acid metabolism. This finding provides novel insights into the regulatory mechanism underlying biofilm formation and highlights potential targets for the development of future antibacterial strategies.</div></div><div><h3>Significance statement</h3><div>This study elucidates the critical role of the <em>eamB</em> gene in <em>Aeromonas hydrophila</em>, a significant aquatic pathogen, by demonstrating its impact on biofilm formation and physiological traits. Through comparative proteomic analysis, we identified 616 differentially abundant proteins in the <em>ΔeamB</em> mutant, revealing its involvement in key metabolic pathways such as amino acid metabolism, flagellar assembly, and fatty acid degradation. Notably, <em>eamB</em> deletion enhanced biofilm formation, while exogenous amino acids like cysteine and <em>O</em>-acetylserine obviously increased biofilm formation in the Δ<em>eamB</em> strain. These findings highlight EamB as a regulator of biofilm formation, offering novel molecular insights into bacterial pathogenicity. This research advances our understanding of biofilm-associated antibiotic resistance and provides potential targets for developing strategies to mitigate infections caused by <em>A. hydrophila</em> in aquaculture and public health.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105510"},"PeriodicalIF":2.8,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics analysis reveal early event molecular effectors of anti-CD19 CAR-T cell therapy in hematological cancer","authors":"John Oluwafemi Teibo ,&nbsp;Roberta Maraninchi Silveira ,&nbsp;Virginia Campos Silvestrini ,&nbsp;Izadora Archiolli ,&nbsp;Ana Paula Masson ,&nbsp;Beatriz Pereira de Morais ,&nbsp;Dayane Schmidt ,&nbsp;Matheus Henrique dos Santos ,&nbsp;Germano Aguiar Ferreira ,&nbsp;Carolina Hassibe Thomé ,&nbsp;Dominic Helm ,&nbsp;Raja Sekhar Nirujogi ,&nbsp;Dairo Renato Alessi ,&nbsp;Virginia Picanço-Castro ,&nbsp;Lucas Eduardo Botelho de Souza ,&nbsp;Vitor Marcel Faça","doi":"10.1016/j.jprot.2025.105507","DOIUrl":"10.1016/j.jprot.2025.105507","url":null,"abstract":"<div><div>Chimeric antigen receptor T-cell (CAR-T) therapy is at the forefront of the field of cell immunotherapy. In this study, we generated an anti-CD19 CAR-Jurkat T cell line using a locally produced second-generation anti-CD19 CAR construct, which allowed us to analyse early proteomic changes that are crucial for comprehending the signalling pathways and mechanism of action of this CAR-T cell. SILAC-heavy tagged Raji B-cells and anti-CD19 CAR-Jurkat T-cells were co-cultured for ten minutes. The proteomic profiles were acquired via DIA methodology on the Orbitrap Astral LC-MS/MS platform. The proteome was extensively covered, resulting in about 8800 protein identifications at 1 % FDR. The effector CAR-Jurkat cells showed proteomic changes involving antigen presentation by CD74. The target Raji B-cells exhibited more significant alterations. Effector proteins, namely CD247, CD28, DAP, LCK, p38 MAPK, and CASP3, were validated, as they have critical roles in antigen presentation, T-cell activation, and apoptosis. Pharmacological inhibition of LCK using Dasatinib further suggested its pivotal role in early CAR-T signalling. This study led us to identify proteins that function as molecular effectors of anti-CD19 CAR-T cell therapy during the initial phases of CAR-T-target cell engagement, advancing our knowledge of the mechanism and signalling pathways that will support CAR-T cell development.</div></div><div><h3>Significance</h3><div>Chimeric antigen receptor T-cell (CAR-T cell) therapy is state-of-the-art in cell and immunotherapy. Determining important players in cellular communication and signalling mediated by membranes and intracellular proteins requires understanding the connection between tumours and modified cells. We employed global proteomics in this study to better grasp the functional protein networks using a high-sensitivity mass spectrometric platform for protein identification and quantification. We identified proteins as molecular effectors of anti-CD19 CAR-T cell treatment during the early stages of CAR-T-target cell interaction. Our understanding of the mechanism and signalling pathways will promote the development of new CAR constructs and improve the efficacy and ability to overcome the resistance of this innovative cancer treatment strategy, which will advance the identification of adjuvant molecules for the regulation of CAR-T responses.</div></div>","PeriodicalId":16891,"journal":{"name":"Journal of proteomics","volume":"321 ","pages":"Article 105507"},"PeriodicalIF":2.8,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144731928","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}