Journal of Proteome Research最新文献_第9页

Correction to “Dynamics of Single-Cell Protein Covariation during Epithelial–Mesenchymal Transition” 对“上皮-间质转化过程中单细胞蛋白共变动力学”的修正。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-11 DOI: 10.1021/acs.jproteome.6c00618

Saad Khan, Rachel Conover, Anand R. Asthagiri, Nikolai Slavov

引用次数: 0

Targeted Modulation of Abundant Proteins Enhances Proteomic Profiling of Ovarian Cancer Ascites: A Pilot Technical Workflow Comparison 靶向调节丰富的蛋白质增强卵巢癌腹水的蛋白质组学分析：一个试点技术工作流程比较

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-19 DOI: 10.1021/acs.jproteome.6c00382

Zongkai Peng, James Lausen, Doris M. Benbrook, Zhibo Yang, Nagib Ahsan

{"title":"Targeted Modulation of Abundant Proteins Enhances Proteomic Profiling of Ovarian Cancer Ascites: A Pilot Technical Workflow Comparison","authors":"Zongkai Peng, James Lausen, Doris M. Benbrook, Zhibo Yang, Nagib Ahsan","doi":"10.1021/acs.jproteome.6c00382","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00382","url":null,"abstract":"Ascites from ovarian cancer patients are increasinglyrecognizedas a valuable biofluid for cancer research, as its protein compositionreflects the disease state and may reveal biomarkers of treatmentsensitivity and response. However, the detection of low-abundanceproteins is hindered by the presence of highly abundant proteins suchas albumin. In this study, we evaluated five protein preparation methodsfor their effectiveness in depleting high-abundance or enriching low-abundanceproteins in ovarian cancer ascites. The Norgen (Nor), Minutes (Min),and Perchloric acid (PerCA) methods were based on abundant proteindepletion, while the Urine (Uri) and Nanomics (Nano) kits focusedon low-abundance protein enrichment. Processed samples were analyzedusing label-free quantitative bottom-up proteomics by LC-MS/MS, followedby a bioinformatics assessment. Compared with undepleted ascites (UnD),Min, Nor, Nano, and PerCA increased protein identifications, whereasUri produced profiles similar to those of UnD. Notably, PerCA andNano enabled the identification of distinct protein subsets associatedwith cancer-related pathways, including immune responses and autophagy.PerCA enriched transmembrane and secreted immunomodulatory glycoproteins,whereas Nano enrichment primarily captured secreted, nuclear, andcytoplasmic soluble proteins. Overall, our results show that bothhigh-abundance protein depletion and low-abundance enrichment improveascites proteome coverage, each offering distinct advantages in identifyingbiologically relevant low-abundance proteins.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"5011–5021"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890317","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}

引用次数: 0

Antivenomic and Proteomic Assessment of Inter- and Intrapopulation Venom Variations in Nikolsky’s Adder Vipera nikolskii: Comparison to Common Adder Vipera berus 尼古斯基蝰蛇种群内和种群间毒液变异的抗蛇毒学和蛋白质组学研究：与普通蝰蛇的比较

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-22 DOI: 10.1021/acs.jproteome.6c00088

Elena Gondarenko, Igor Ivanov, Polina Arkhangelskaya, Alena Timakina, Vladimir Pavlov, Igor Dyachenko, Vladislav Starkov, Igor Kasheverov, Yuri Utkin, Victor Tsetlin, Denis Kudryavtsev

{"title":"Antivenomic and Proteomic Assessment of Inter- and Intrapopulation Venom Variations in Nikolsky’s Adder Vipera nikolskii: Comparison to Common Adder Vipera berus","authors":"Elena Gondarenko, Igor Ivanov, Polina Arkhangelskaya, Alena Timakina, Vladimir Pavlov, Igor Dyachenko, Vladislav Starkov, Igor Kasheverov, Yuri Utkin, Victor Tsetlin, Denis Kudryavtsev","doi":"10.1021/acs.jproteome.6c00088","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00088","url":null,"abstract":"Snake venom variation has importantclinical implications,yetindividual-level venomics remains limited. We investigated inter-and intrapopulation variability in forest-steppe adder Vipera nikolskii and its recognition by commercial V. berus antivenom using proteomic and immunologicalapproaches. Venoms from 12 individual V. nikolskii specimens representing two geographically distinct populations (BGand KM), together with three pooled V. nikolskii and one pooled V. berus samples wereanalyzed by LC–MS/MS, ELISA, Western blot, and pull-down assays.Multivariate analysis revealed relative homogeneity in BG and pronouncedheterogeneity in KM venoms. Area-based proteomics revealed V. berus venom enrichment in PLA2 (34.6%),SVMP (14.6%), and CRiSP (15.6%), whereas V. nikolskii venoms were more variable. Pooled V. nikolskii venoms showed SVMP abundance (35.2–41.1%), contrasting withlower levels in individual samples. Antivenom binding was strongerfor V. berus but weaker and more variableacross individual and pooled V. nikolskii samples. Antivenom targeted PLA2/VEGF, CRiSP (only in V. berus), and Kunitz-type proteins. In vivo neutralization assay demonstrated strong protection against V. berus but not V. nikolskii venom. These findings reveal substantial compositional and antigenicvariability in V. nikolskii venoms,highlight discrepancies between pooled and individual ones, and underscorethe need for region-specific and functionally validated antivenomevaluation.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4546–4562"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890334","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}

引用次数: 0

Targeting Arginine Metabolism via ArcR: Blestriarene B Suppresses Staphylococcus aureus Biofilm Formation and Cellular ATP Production 通过ArcR靶向精氨酸代谢：Blestriarene B抑制金黄色葡萄球菌生物膜形成和细胞ATP生成

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-11 DOI: 10.1021/acs.jproteome.6c00236

Huan-Huan Wang, Yan Ju, Ying Liu, Min Jiang, Huan Yao, Shulong Zhao, Guozhen Cui, Tian-Peng Yin, Ze Wang, Gao-Fei Du, Xiao-Yan Yang

{"title":"Targeting Arginine Metabolism via ArcR: Blestriarene B Suppresses Staphylococcus aureus Biofilm Formation and Cellular ATP Production","authors":"Huan-Huan Wang, Yan Ju, Ying Liu, Min Jiang, Huan Yao, Shulong Zhao, Guozhen Cui, Tian-Peng Yin, Ze Wang, Gao-Fei Du, Xiao-Yan Yang","doi":"10.1021/acs.jproteome.6c00236","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00236","url":null,"abstract":"Blestriarene B (BB), a biphenanthrene compound isolatedfrom themedicinal plant Bletilla striata, possessesantibacterial properties against Staphylococcus aureus; however, its molecular target and underlying mechanisms remainunclear. Arginine metabolism plays a pivotal role in antibiotic susceptibilityand biofilm development, making this pathway an attractive therapeutictarget. Here, we demonstrate that blestriarene B exerts potent antibacterialactivity against S. aureus both in vitro and in vivo. Data-independentacquisition (DIA) proteomics analysis suggests that the antibacterialmechanism of blestriarene B involves an interaction with the HTH-typetranscriptional regulator ArcR, which is a key regulator of argininecatabolism. Comparative analyses between wild-type and arcR-deficient S. aureus strains confirmedthat ArcR is the molecular target of blestriarene B. Further mechanisticstudies revealed that blestriarene B inhibits biofilm formation, impairscellular ATP production, and ultimately induces bacterial death bybinding to ArcR. Collectively, these findings identify blestriareneB as a promising antibacterial drug and validate ArcR as a novel targetfor anti-S. aureus therapeutics.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4757–4771"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890313","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}

引用次数: 0

Antibody-Based Proximity Labeling Reveals Bait-Proximal Proteomes in Paraffin-Embedded and Snap-Frozen Tissue Samples 基于抗体的接近标记揭示了石蜡包埋和快速冷冻组织样品中的诱饵近端蛋白质组

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-11 DOI: 10.1021/acs.jproteome.6c00086

Inge de Krijger, Tilly W. Aalders, Michiel Vermeulen, Maria V. Luna-Velez

{"title":"Antibody-Based Proximity Labeling Reveals Bait-Proximal Proteomes in Paraffin-Embedded and Snap-Frozen Tissue Samples","authors":"Inge de Krijger, Tilly W. Aalders, Michiel Vermeulen, Maria V. Luna-Velez","doi":"10.1021/acs.jproteome.6c00086","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00086","url":null,"abstract":"Proximity-based labeling approaches have proven highlyvaluablefor uncovering protein–protein interactions, yet their applicationto primary patient material remains challenging. Here, we presenta workflow enabling the use of the antibody-based ProtA-Turbo proximitylabeling system in both formalin-fixed paraffin-embedded (FFPE) andsnap-frozen tissue specimens. Our method efficiently directs biotinylationto diverse antibody baits across tissues of different origins. Downstreammass spectrometry-based proteomics analyses demonstrate the specificityof the method by profiling the proximal proteome of H3K27ac-markedchromatin, the nuclear lamina-associated protein EMD, and the Ser2-phosphorylatedPOLR2A subunit of RNA polymerase II. Using this method, we identifiedcell-type-specific factors and transcriptional regulators in salivarygland carcinoma, healthy testis, and testicular cancer tissue sections.The ability to detect disease-associated complexes directly withintheir native, spatially resolved cellular context using ProtA-Turbocan provide new insights into the molecular basis of human diseaseand may reveal novel, potentially actionable factors with translationalrelevance.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4563–4576"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890314","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}

引用次数: 0

Global Incorporation of a Photo-Cross-Linking Amino Acid to Probe the Protein Interactome under Physiological Conditions 光交联氨基酸在生理条件下探测蛋白质相互作用组的全局整合

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-21 DOI: 10.1021/acs.jproteome.6c00388

Piyoosh Sharma, Divya Yadav, Anneliese M. Faustino, Edgar Manriquez-Sandoval, Mirko Wagner, Thomas Carell, Stephen D. Fried

{"title":"Global Incorporation of a Photo-Cross-Linking Amino Acid to Probe the Protein Interactome under Physiological Conditions","authors":"Piyoosh Sharma, Divya Yadav, Anneliese M. Faustino, Edgar Manriquez-Sandoval, Mirko Wagner, Thomas Carell, Stephen D. Fried","doi":"10.1021/acs.jproteome.6c00388","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00388","url":null,"abstract":"Cross-linking mass spectrometry (XL-MS) has advancedas a powerfulapproach to map protein–protein interactions in cells. Withrecent advances in cross-linkers, instrumentation, and software, interactionscan be observed in a proteome-wide fashion at residue-level resolution.In most XL-MS experiments, a chemical cross-linker possessing twoelectrophiles is added to a biological sample and records spatialinformation by forming covalent bonds between two proximal nucleophilicresidues. On the other hand, photo-cross-linking amino acids thatcan be incorporated into proteins via ribosomal synthesis possessthe capacity to rapidly capture transient protein–protein interactionsunder physiological conditions without introducing exogenous reactivespecies. Diazirine-based photoamino acids have been widely used forthis purpose due to their small size and broad reactivity. Recentstudies have shown that diazirines can form MS-cleavable linkageswhen they react with acidic residues. However, confident interpretationof the resulting spectra and localization of cross-linking sites remainchallenging, limiting broader application of diazirine-based approachesin proteome-wide cross-linking analyses. Here, we address this limitationby leveraging DizPK, a diazirine-containing lysine analog with a dedicatedMS-cleavable urea functionality. We demonstrate proteome-wide incorporationof DizPK in Escherichia coli via stochasticorthogonal recoding of translation and subsequent identification ofphoto-cross-linked peptides to map protein–protein interactionsunder physiological conditions. We find that the resulting approachcan provide high-resolution structural information associated withtransient biological processes.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4870–4887"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890292","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}

引用次数: 0

Benchmarking the OptiSpray−μPAC Workflow against a Traditional Nanospray Capillary Interface for Multiplexed Quantitative Proteomics OptiSpray−μPAC工作流对传统Nanospray毛细管接口进行多路定量蛋白质组学的基准测试

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-26 DOI: 10.1021/acs.jproteome.6c00473

Katherine L. Walker, Christina B. Schroeter, Runsheng Zheng, Joshua A. Silveira, Eloy R. Wouters, Joao A. Paulo

{"title":"Benchmarking the OptiSpray−μPAC Workflow against a Traditional Nanospray Capillary Interface for Multiplexed Quantitative Proteomics","authors":"Katherine L. Walker, Christina B. Schroeter, Runsheng Zheng, Joshua A. Silveira, Eloy R. Wouters, Joao A. Paulo","doi":"10.1021/acs.jproteome.6c00473","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00473","url":null,"abstract":"Nanoflowliquid chromatography coupled with tandem mass spectrometry(LC–MS/MS) underpins modern quantitative proteomics, yet thecolumn-to-mass spectrometer interface remains an important yet oftenunderappreciated determinant of analytical depth, sensitivity, andreproducibility. Here, we benchmark an integrated workflow comprisingthe newly developed OptiSpray ion source and a micropillar array column(μPAC) cartridge against a conventional Nanospray Flex Sourcewith an Accucore resin-packed capillary column. We performed a TMTpro18-plex experiment across nine human cell lines on a FAIMS Pro-equippedOrbitrap Exploris 480. Following basic-pH reversed-phase fractionation,12 fractions were analyzed on both workflow configurations under matchedchromatographic gradient and acquisition conditions. Across both configurations,we quantified >9000 protein groups with highly comparable quantitativereproducibility and principal component clustering. Direct comparisonof protein abundance ratios across cell lines showed agreement (Pearson R2 ≈ 0.7–0.8) without systematicbias. These results were achieved without workflow-specific optimizationof the OptiSpray−μPAC platform, enabling direct transferof established acquisition methods. Despite differences in columnarchitecture, both configurations delivered comparable proteome coverageand quantitative fidelity. These findings establish the OptiSpray−μPACworkflow as a standardized alternative to conventional capillary-basedinterfaces, offering simplified operation while preserving quantitativeperformance.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4987–4999"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890339","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}

引用次数: 0

Unlocking the Circulating Proteome: Toward Clinical Translation 解锁循环蛋白质组：走向临床翻译

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-17 DOI: 10.1021/acs.jproteome.6c00277

Sara Ahadi, Haris Babačić, Lee S. Cantrell, Daniel Hornburg, Johannes B. Müller-Reif, Laura F. Dagley, Ida Chiara Guerrera, Vincent Albrecht, Fredrik Edfors, Xiaobo Yu, Zhi Sun, Robert L. Moritz, Frank Schmidt, Stefanie M. Hauck, Eric W. Deutsch, Gilbert S. Omenn, Jochen M. Schwenk, Philipp E. Geyer

{"title":"Unlocking the Circulating Proteome: Toward Clinical Translation","authors":"Sara Ahadi, Haris Babačić, Lee S. Cantrell, Daniel Hornburg, Johannes B. Müller-Reif, Laura F. Dagley, Ida Chiara Guerrera, Vincent Albrecht, Fredrik Edfors, Xiaobo Yu, Zhi Sun, Robert L. Moritz, Frank Schmidt, Stefanie M. Hauck, Eric W. Deutsch, Gilbert S. Omenn, Jochen M. Schwenk, Philipp E. Geyer","doi":"10.1021/acs.jproteome.6c00277","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00277","url":null,"abstract":"Blood-based proteomics is approaching a translationalinflectionpoint. Driven by advances in measurement technologies, rapid expansionof analytical capabilities, and growing adoption across research andmedical communities, there is increasing demand for clinically actionablebiomarkers. As the field transitions away from purely large-scalediscovery-oriented studies toward more informed, targeted, application-drivenanalyses, the generation of proteomic data is no longer the bottleneck.Instead, the central challenge is to translate these measurementsinto robust, reproducible, and clinically meaningful insights. Inthis Review, we assess recent technological and methodological developments,evaluate persistent preanalytical and interpretative limitations,and outline the key steps required for clinical translation. We focuson three deeply interconnected dimensions: the capabilities and constraintsof current measurement platforms, the role of computational and machinelearning approaches in extracting biological and clinical signals,and the emergence of large-scale population studies that create newopportunities for validation and generalization. Finally, we discussa forward-looking vision in which proteomics plays a central rolein dynamic, multilayered omics frameworks, where integration withgenomics, temporal profiling, and imaging can deepen our understandingof health, disease, and therapeutic response.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4367–4379"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148885580","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}

引用次数: 0

Comprehensive Landscape of Post-Translational Modification Alterations in Nephrolithiasis Revealing Activation of Multiple Cell Death Pathways 肾结石翻译后修饰改变的综合景观揭示了多种细胞死亡途径的激活

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-11 DOI: 10.1021/acs.jproteome.6c00230

Yining Dong, Mengya Zhang, Yang Xu, Jianchao Zhang, Changjuan Wang, Xiaolu Zhang, Yongliang Ni

{"title":"Comprehensive Landscape of Post-Translational Modification Alterations in Nephrolithiasis Revealing Activation of Multiple Cell Death Pathways","authors":"Yining Dong, Mengya Zhang, Yang Xu, Jianchao Zhang, Changjuan Wang, Xiaolu Zhang, Yongliang Ni","doi":"10.1021/acs.jproteome.6c00230","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00230","url":null,"abstract":"Nephrolithiasis is a common urinary disorder characterizedby highprevalence and recurrence, but the molecular mechanisms underlyingcalcium oxalate (CaOx)-crystal-induced renal injury remain incompletelyunderstood. We applied integrated proteomic, phosphoproteomic, acetylomic,and lactylomic analyses to kidney tissues from a mouse model of CaOxnephrolithiasis followed by bioinformatic analysis and experimentalvalidation. We identified 658 differentially expressed proteins, 735differential phosphorylation sites, 335 differential acetylation sites,and 113 differential lactylation sites. Functional enrichment indicatedimmune activation, fibrotic remodeling, and alterations in PI3K-Akt,NOD-like receptor, p53, and Toll-like receptor signaling togetherwith changes in fatty acid degradation, the tricarboxylic acid cycle,and glycolysis. Kinase activity prediction suggested the relativeactivation of multiple cyclin-dependent kinases. Proteins associatedwith ferroptosis, autophagy, necroptosis, and pyroptosis, includingACSL4, BNIP3, RIPK3, and GSDMD, showed coordinated abundance and modificationchanges. Several candidate sites, including MTOR_S1849, GCLM_K94,GCLM_S59, and GSS_K172, were also dysregulated. These data providea multiomics resource for CaOx nephrolithiasis and identify candidatePTM events and regulatory pathways for future mechanistic validation.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4688–4703"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890315","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}

引用次数: 0

Revealing Hidden Variables in DESI-Based Spatial Metabolomics: Solvent Composition and Tissue Type as Critical Drivers 揭示基于desi的空间代谢组学中的隐藏变量：溶剂成分和组织类型是关键驱动因素

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-09-04 Epub Date: 2026-08-08 DOI: 10.1021/acs.jproteome.6c00001

Marco Giampà, Peter D. E. M. Verhaert, Jan Claereboudt, Emmanuelle Claude, Bernard Drotleff, Geert Goeminne, Veerle Heedfeld, Jakub Idkowiak, Emrys A. Jones, Alexander Muck, Janick Mathys, Alaa Othmann, Nina Ravoet, Julio Lopes-Sampaio, Johannes V. Swinnen, Ina Jochmans, Bart Ghesquière

{"title":"Revealing Hidden Variables in DESI-Based Spatial Metabolomics: Solvent Composition and Tissue Type as Critical Drivers","authors":"Marco Giampà, Peter D. E. M. Verhaert, Jan Claereboudt, Emmanuelle Claude, Bernard Drotleff, Geert Goeminne, Veerle Heedfeld, Jakub Idkowiak, Emrys A. Jones, Alexander Muck, Janick Mathys, Alaa Othmann, Nina Ravoet, Julio Lopes-Sampaio, Johannes V. Swinnen, Ina Jochmans, Bart Ghesquière","doi":"10.1021/acs.jproteome.6c00001","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00001","url":null,"abstract":"In the development of a desorption electrospray ionization(DESI)workflow for spatial metabolomics, we investigated the impact of twocommonly used solvent systems, 90% acetonitrile (ACN) and 90% methanol(MeOH), on the spatial metabolomic profiling of various murine tissues.The performance of both solvents was evaluated across several metaboliteclasses (central carbon metabolites, amino acids, and fatty acids).Although the ACN-based solvent system led to higher signal intensitiesfor small polar metabolites involved in glycolysis, the tricarboxylicacid (TCA) cycle, and amino acid metabolism, the MeOH-based solventsystem provided superior signal intensities for fatty acids. Thesefindings demonstrate that the solvent composition differentially influencesmetabolite extraction and ionization processes in DESI and shouldbe carefully matched to the biological questions and metabolite classesof interest. As a proof-of-principle, the ACN solvent system was appliedto a pilot study based on a rat model of renal ischemic injury, revealingregion-specific metabolic changes between normoxic and ischemic conditions.Together, these results demonstrate the importance of solvent selectionin DESI-based spatial metabolomics and showcase the ability of thisapproach to uncover spatially resolved metabolic adaptations associatedwith tissue injury.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 9","pages":"4614–4623"},"PeriodicalIF":3.8,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148890303","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}

引用次数: 0