Journal of Proteome Research最新文献_第3页

Leveraging Urinary Proteomics to Advance Pathophysiologic and Biomarker Perspectives of Chronic Kidney Disease in Cats 利用尿蛋白质组学来推进猫慢性肾脏疾病的病理生理学和生物标志物观点

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-10-14 DOI: 10.1021/acs.jproteome.6c00357

Katelyn B. Brusach, Ariana E. Shannon, Brian C. Searle, Jessica M. Quimby

{"title":"Leveraging Urinary Proteomics to Advance Pathophysiologic and Biomarker Perspectives of Chronic Kidney Disease in Cats","authors":"Katelyn B. Brusach, Ariana E. Shannon, Brian C. Searle, Jessica M. Quimby","doi":"10.1021/acs.jproteome.6c00357","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00357","url":null,"abstract":"Chronic kidney disease (CKD) is one of the most prevalentdiseasesin feline medicine. Mass spectrometry-based urinary proteomics offerspowerful insight into biomarker candidates and disease subtyping inCKD by measuring protein profiles rather than individual proteins.This study aims to measure the urinary proteome to identify proteinprofiles in cats with and without CKD to gain pathophysiological insightsinto the disease and more precisely diagnose CKD. Here, we identify2,219 urinary proteins in the feline urinary proteome. Using univariatebiomarker analysis, we show that MMP-7 may be a promising biomarkerof CKD in cats. We then demonstrate the power of using protein profilesrather than individual proteins by grouping proteins based on howthey trend across disease states. The changes to the global urinaryproteomes of individual cats showed three distinct groups of CKD catswith unique protein profiles, suggesting that different pathophysiologicalmechanisms mediate disease subtypes. We demonstrate that large-scaleurinary proteomics may provide a powerful framework for discoveringcandidate biomarkers that advance the subtyping and mechanistic understandingof feline CKD.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"5862–5872"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330300","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

Transcriptomics-Coupled Proteomics Identifies CD36 as a Potential Radiation-Responsive Biomarker in Macrophages 转录组学-偶联蛋白质组学鉴定CD36是巨噬细胞中潜在的辐射应答生物标志物

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-09-24 DOI: 10.1021/acs.jproteome.6c00472

Yonglong Yu, Dongwei Guan, Yaoying Long, Pengju Huang, Lu Wang, Xinlei Liu, Huishan Wang, Jinyi Liu, Xiaolong Tian, Yimei Feng, Shijie Yang, Xi Zhang

{"title":"Transcriptomics-Coupled Proteomics Identifies CD36 as a Potential Radiation-Responsive Biomarker in Macrophages","authors":"Yonglong Yu, Dongwei Guan, Yaoying Long, Pengju Huang, Lu Wang, Xinlei Liu, Huishan Wang, Jinyi Liu, Xiaolong Tian, Yimei Feng, Shijie Yang, Xi Zhang","doi":"10.1021/acs.jproteome.6c00472","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00472","url":null,"abstract":"The therapeutic effect of radiotherapy is greatly hinderedby radiationinjury, primarily driven by a dysfunctional immune microenvironment.Macrophages play an essential role in regulating the radiation response,but their intrinsic mechanism is not fully understood. In this study,we aimed to identify key molecular targets underlying macrophage responsesto radiation using omics technologies including transcriptomics andproteomics. We found that the mRNA and protein expression levels ofthe scavenger receptor CD36 (also known as fatty acid translocase)were significantly upregulated following radiation exposure in boththe murine macrophage cell line RAW264.7 and primary mouse bone-marrow-derivedmacrophages. Additionally, in vivo experiments alsoconfirmed a significant increase in the level of expression of CD36in macrophages derived from mice exposed to radiation. Pharmacologicalinhibition of CD36 promoted radiation-induced macrophage apoptosisand inflammatory responses, indicating potential radioprotective andanti-inflammatory effects. These findings suggest that CD36 upregulationis a prominent feature of macrophages in response to radiation exposure,thereby highlighting its potential as a therapeutic target for mitigatingradiation-induced injury.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"6031–6042"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330239","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

Integrated Transcriptomic and Proteomic Analysis Reveals Antibacterial Responses of Staphylococcus aureus to 60Co γ-Irradiation 综合转录组学和蛋白质组学分析揭示了金黄色葡萄球菌对60Co γ-辐照的抗菌反应

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-09-30 DOI: 10.1021/acs.jproteome.6c00340

Long Cui, Zehui Si, Yi Wei, Xian Wang, Huili Yan, Sisi Chen

{"title":"Integrated Transcriptomic and Proteomic Analysis Reveals Antibacterial Responses of Staphylococcus aureus to 60Co γ-Irradiation","authors":"Long Cui, Zehui Si, Yi Wei, Xian Wang, Huili Yan, Sisi Chen","doi":"10.1021/acs.jproteome.6c00340","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00340","url":null,"abstract":"γ-Irradiation is a widely usednonthermal sterilizationtechnologyin food processing; however, the mechanisms underlying γ-irradiation-inducedinactivation of Staphylococcus aureus (S. aureus) remain incompletely understood. This studyinvestigated the effects of 60Co γ-irradiation on S. aureus and its molecular responses byintegrating physiological assays with transcriptomic and proteomicanalyses. γ-Irradiation produced a dose-dependent reductionin bacterial culturability from 0 to 2.0 kGy, with the greatest reductionobserved at 2.0 kGy. Although no obvious surface morphological alterationswere detected by scanning electron microscopy, γ-irradiationcompromised membrane integrity, as evidenced by increased leakageof nucleic acids, proteins, and K+ and decreased ATPase-associatedactivities. Integrated omics analysis identified 486 differentiallyexpressed genes and 178 differentially expressed proteins following2.0 kGy irradiation. Functional enrichment analysis revealed alterationsin pathways associated with cell envelope biosynthesis, amino acidmetabolism, and energy metabolism. Notably, upregulation of MNH antiporterssuggested a potential adaptive response to maintain cellular ion homeostasisunder irradiation stress. Collectively, these findings indicate thatγ-irradiation induces S. aureus inactivation through multiple cellular alterations, including membranedysfunction, genomic damage, intracellular leakage, and metabolicdisturbances.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"6018–6030"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330314","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

Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics Using Controlled Quantitative Experiments (CQEs) 使用受控定量实验（CQEs）的定量数据独立获取（DIA）蛋白质组学建议

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-10-22 DOI: 10.1021/acs.jproteome.6c00328

Andrew M. Frey, Frances Sidgwick, Andrew Porter, Pawel Palmowski, Matthias Trost

{"title":"Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics Using Controlled Quantitative Experiments (CQEs)","authors":"Andrew M. Frey, Frances Sidgwick, Andrew Porter, Pawel Palmowski, Matthias Trost","doi":"10.1021/acs.jproteome.6c00328","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00328","url":null,"abstract":"Advances in mass spectrometry and associated computationaltoolshave resulted in the widespread adoption of Data-Independent Acquisition(DIA) for proteomics. Experiments using state-of-the-art instrumentationand specialized modes of acquisition report ever-increasing throughputand protein identification rates. However, experiments to test theefficacy of protein quantitation in these novel methods are surprisinglyrare, especially in novel methods where low sample input or high throughputis considered. Here, we performed a series of controlled quantitativeexperiments (CQEs) on two commonly used mass spectrometry platforms(Exploris480 and timsTOF HT), using defined mixtures of human, yeast,and bacterial proteomes. Peptide spectrum matching and initial quantificationwere performed using DIA-NN, with a series of postprocessing optionsalso compared. Overall, we identified >10,000 unique proteins and>160,000 precursors across samples with excellent accuracy andprecision.Additional postprocessing was found to have drastic impacts on IDrates, quantitative precision and accuracy, and false quantitativerate (FQR). These impacts were particularly notable in experimentsusing low amounts of sample. In optimal loading conditions, data processingcould reduce FQR from ∼0.1 to 0% with minimal losses in IDrates. Ultimately, we present a series of recommendations for proteomicsdata processing and advice on the use of CQEs and resulting metricswhen assessing quantitative efficacy in novel modes of acquisition.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"5817–5830"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330315","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

High-Resolution Spatial Proteomics Uncovers Molecular Diversity across Mouse Hippocampal Subregions 高分辨率空间蛋白质组学揭示小鼠海马亚区分子多样性

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-10-23 DOI: 10.1021/acs.jproteome.6c00286

Zhangyang Xu, Jessie Shi, Reta Birhanu Kitata, Rui Zhao, Rosalie K Chu, Sehong Min, Wei-Jun Qian, Song-Lin Ding, Tujin Shi, Tong Zhang

{"title":"High-Resolution Spatial Proteomics Uncovers Molecular Diversity across Mouse Hippocampal Subregions","authors":"Zhangyang Xu, Jessie Shi, Reta Birhanu Kitata, Rui Zhao, Rosalie K Chu, Sehong Min, Wei-Jun Qian, Song-Lin Ding, Tujin Shi, Tong Zhang","doi":"10.1021/acs.jproteome.6c00286","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00286","url":null,"abstract":"The hippocampus (HP) is a structurally and functionallyheterogeneousbrain region critical for learning, memory, and spatial navigation.Although transcriptomic studies have revealed subregion-specific geneexpression patterns, the corresponding high-resolution spatial proteomiclandscape remains largely unexplored. Here, we applied a single-voxelproteomics workflow at 50 μm resolution to profile the proteincomposition of HP subregions, including the dentate gyrus (DG) andCornu Ammonis fields 1–3 (CA1–CA3). Across the foursubregions, we identified over 2,200 protein groups and found bothconserved and region-specific proteins. Differential expression andnetwork analyses revealed molecular signatures associated with specificsubregions, including synaptic plasticity in CA1, mitochondrial metabolismin CA2, cytoskeletal organization and protein homeostasis in CA3,and excitatory signaling in DG. Integration with transcriptomic dataconfirmed consistent region-enriched markers at both the gene andprotein levels, including Homer1 and Itpka in CA1, Homer3 in CA3,and Calb1/2 in DG. Thus, our data set demonstrates subregion-specificmolecular specialization at the proteome level and provides a high-resolutionresource to link structural, functional, and metabolic diversity inthe hippocampus. Further application of our high-resolution spatialproteomics will lay the foundation for studying HP development, circuitfunction, and disease-associated proteomic alterations.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"5792–5803"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330359","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

A High-Throughput and In-Depth Coverage Proteomic Analysis Workflow Using SLIM-Based High-Resolution Ion Mobility Spectrometry-Mass Spectrometry 一个高通量和深度覆盖蛋白质组学分析工作流程使用基于薄的高分辨率离子迁移谱-质谱

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-10-18 DOI: 10.1021/acs.jproteome.6c00116

Jung Yun Lee, Dylan H. Ross, Yuqian Gao, Matthew J. Gaffrey, Carrie D. Nicora, Priscila M. Lalli, Adam L. Hollerbach, Sandilya V. B. Garimella, Daniel J. Orton, Thomas L. Fillmore, Ronald J. Moore, Aivett Bilbao, Yehia M. Ibrahim, Tujin Shi, Richard D. Smith, Xueyun Zheng

{"title":"A High-Throughput and In-Depth Coverage Proteomic Analysis Workflow Using SLIM-Based High-Resolution Ion Mobility Spectrometry-Mass Spectrometry","authors":"Jung Yun Lee, Dylan H. Ross, Yuqian Gao, Matthew J. Gaffrey, Carrie D. Nicora, Priscila M. Lalli, Adam L. Hollerbach, Sandilya V. B. Garimella, Daniel J. Orton, Thomas L. Fillmore, Ronald J. Moore, Aivett Bilbao, Yehia M. Ibrahim, Tujin Shi, Richard D. Smith, Xueyun Zheng","doi":"10.1021/acs.jproteome.6c00116","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00116","url":null,"abstract":"Comprehensive proteome profiling requires improved depthand throughput,which have traditionally relied on advances in mass spectrometry (MS)and chromatographic separation. Here, we present fracSLIM, a high-throughput, deep-coverage proteomics workflow that integratesstructures for lossless ion manipulation (SLIM)-based high-resolutionion mobility spectrometry–mass spectrometry (IMS-MS) with offlinepeptide fractionation. This approach leverages ion mobility-derivedinformation, including enhanced separation of isomeric and isobaricspecies and accurate collision cross-section (CCS) measurements, toenable confident peptide identification. We evaluated the utilityof this approach for complex proteomics samples by analyzing threefractions of peptide digests from human HeLa cells, enabling an over10-fold increase in peptide identifications compared to conventionalsingle-shot LC-MS workflows while maintaining high reproducibility.Furthermore, the workflow supports quantitative analysis by comparingendogenous peptides to heavy-isotope-labeled standards. These resultshighlight the potential of fracSLIM for greatly improvedhigh-throughput and deep proteome profiling of complex samples.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"6003–6017"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330373","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

Automating Large-Scale Experiment Scheduling and Planning with the WorkListGenerator 自动化大规模实验调度和计划与WorkListGenerator

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-09-26 DOI: 10.1021/acs.jproteome.6c00362

Parker S. Reyes, Gabriel B. Wilson, Ivin C. Tait, Caleb T. Coons, Hsien-Jung L. Lin, Ryan T. Kelly, Samuel H. Payne

{"title":"Automating Large-Scale Experiment Scheduling and Planning with the WorkListGenerator","authors":"Parker S. Reyes, Gabriel B. Wilson, Ivin C. Tait, Caleb T. Coons, Hsien-Jung L. Lin, Ryan T. Kelly, Samuel H. Payne","doi":"10.1021/acs.jproteome.6c00362","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00362","url":null,"abstract":"As proteomics capabilitieshave grown increasingly robust,biologicalexperiments and hypotheses investigating hundreds or thousands ofsamples are now possible. With an increase in project scale, bothexperimental design and metadata management become major bottlenecks.Of particular importance in this data management process is the generationof instrument scheduling files for both LC and MS instruments, especiallythe randomization of the run ordering to prevent batch artifacts thatwould confound the experimental hypothesis. Although best practicesfor blocking and randomization exist, this is frequently done by hand─atedious and error-prone task. We present a software tool, WorkListGenerator,that captures core project metadata in a structured format, performsblock randomization, and produces instrument worklists for LC-MS.The tool is flexible to various experimental designs common in single-cellproteomics and other large-scale studies and is available as an open-sourcecommand-line tool at https://github.com/RTKlab-BYU/worklist_generation.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"6492–6496"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330241","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

Optimized Proteomic and N-Glycoproteomic Profiling Reveals Aging-Associated Molecular Remodeling in Granulosa Cells 优化的蛋白质组学和n -糖蛋白组学分析揭示了颗粒细胞中与衰老相关的分子重塑

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-10-23 DOI: 10.1021/acs.jproteome.6c00614

Yue Yan, Jiawei Fan, Siheng Yuan, Zhenfei Wu, Jing Wang, Haojie Lu

{"title":"Optimized Proteomic and N-Glycoproteomic Profiling Reveals Aging-Associated Molecular Remodeling in Granulosa Cells","authors":"Yue Yan, Jiawei Fan, Siheng Yuan, Zhenfei Wu, Jing Wang, Haojie Lu","doi":"10.1021/acs.jproteome.6c00614","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00614","url":null,"abstract":"Granulosa cells (GCs) are essential for maintaining thefollicularmicroenvironment and supporting oocyte development. However, the comprehensiveprofiling of the granulosa cell proteome and N-glycoproteomeremains insufficiently characterized. Furthermore, the limited availabilityof clinical granulosa cell samples and the inherent difficulty inextracting membrane and secreted proteins necessitate a standardizedsample preparation protocol. In this study, we systematically evaluatedthree protein extraction workflows (sodium dodecyl sulfate (SDS),sodium deoxycholate (SDC) and urea) alongside different digestionstrategies (trypsin and tandem LysC-trypsin) for granulosa cell proteomicand N-glycoproteomic analyses. The SDS-based workflowshowed superior overall performance and was applied to clinical granulosacell samples from young (n = 6) and aged (n = 6) women. We successfully identified 7599 proteins and4703 N-glycopeptides from the granulosa cell samples.Integrated proteomic and N-glycoproteomic analysesidentified 12 differentially expressed proteins and 111 differentiallyabundant N-glycopeptides between young and aged GCs,suggesting alterations in protein expression and N-glycosylation associated with ovarian aging. Notably, changes in N-glycosylation were observed independently of changes inprotein abundance. This study establishes a robust workflow for comprehensiveproteomic and N-glycoproteomic profiling of clinicalgranulosa cell samples and provides novel insights into ovarian aging.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"6301–6314"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330252","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

Detecting Methylation in MCF7 Cells with a Combination of SCX- and No-Enrichment Methods 结合SCX富集和无富集方法检测MCF7细胞的甲基化

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-10-14 DOI: 10.1021/acs.jproteome.6c00500

Jessica M. Conforti, Charli S. Worth, Amanda M. Ziegler, Hadden K. Swanzy, Rabin Budhathoki, Joseph H. Taube, Elyssia S. Gallagher

{"title":"Detecting Methylation in MCF7 Cells with a Combination of SCX- and No-Enrichment Methods","authors":"Jessica M. Conforti, Charli S. Worth, Amanda M. Ziegler, Hadden K. Swanzy, Rabin Budhathoki, Joseph H. Taube, Elyssia S. Gallagher","doi":"10.1021/acs.jproteome.6c00500","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00500","url":null,"abstract":"Methylation is animportant post-translational modificationthatimpacts cellular processes. Yet, protein methylation remains analyticallychallenging to study by proteomics due to variable methylation stoichiometryand the lack of broadly applicable enrichment strategies, resultingin an underrepresentation of methylated peptides in LC-MS/MS analyses.Although methylation does not alter the physicochemical propertiesof amino acids, there is a reduced probability of trypsin cleavageafter methylated lysine or arginine, leading to increased positivecharges on methylated peptides. Strong cation exchange (SCX) can beused to enrich methylated peptides. However, the number of methylationsites identified with SCX varies across previous studies, likely becauseof the use of different stationary phases and supports, elution strategies,and combinations of multiple enrichment techniques. Therefore, wehypothesize that commercially available SCX tips with an MS-friendlyammonium acetate elution can be used to enrich methylated peptides.Our results show that SCX effectively fractionates peptides by charge,which is associated with the number of missed cleavages, and thatmethylated peptides elute in fractions with high concentrations ofammonium acetate. When comparing SCX and nonenrichment methods, complementarymethylation sites are identified, differing by sequence motifs, cellularcomponent ontologies, and biological process ontologies. Ultimately,these results suggest that both SCX and nonenrichment methods enablethe detection of distinct methylation sites, and a combination ofapproaches may be required to effectively profile the methylome ofcomplex biological samples. Data have been deposited in MassIVE (MSV000098142).","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"6082–6093"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330301","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

Integrated Transcriptomic and Proteomic Analyses Reveal a Diverse Venom Repertoire in Macrothele guizhouensis 整合转录组学和蛋白质组学分析揭示贵州巨鳗多种毒液库

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2026-11-06 Epub Date: 2026-10-08 DOI: 10.1021/acs.jproteome.6c00343

Mengmeng Zhang, Wenhao Yin, Yulin Zheng, Zhi Li, Zhibin Yang, Zizhong Yang

{"title":"Integrated Transcriptomic and Proteomic Analyses Reveal a Diverse Venom Repertoire in Macrothele guizhouensis","authors":"Mengmeng Zhang, Wenhao Yin, Yulin Zheng, Zhi Li, Zhibin Yang, Zizhong Yang","doi":"10.1021/acs.jproteome.6c00343","DOIUrl":"https://doi.org/10.1021/acs.jproteome.6c00343","url":null,"abstract":"Thevenom of spiders in the family Macrothelidae is a rich sourceof bioactive molecules with potential biomedical and agriculturalapplications, yet the venom composition of Macrothele guizhouensis remains poorly understood. Here, integratedtranscriptomic and proteomic analyses were used to characterize itsvenom repertoire. Venom-gland transcriptomics identified diverse toxin-relatedtranscripts, including cysteine-rich peptides (CRPs) and venom-associatedproteins, while proteomics confirmed multiple secreted venom components.RT-qPCR analysis of representative toxin genes provided additionaldescriptive evidence for their expression patterns in the venom gland.Structural and evolutionary analyses revealed both conserved toxinscaffolds shared with related Macrothele speciesand divergent, lineage-specific peptides that may represent noveltoxin variants. Several CRPs displayed structural features resemblingthose of known ion-channel-modulating toxins, including a double-knotpeptide that represents a candidate for future functional investigation.These findings provide the first comprehensive molecular characterizationof M. guizhouensis venom, expand currentknowledge of toxin diversity and evolution in Macrothelidae, and establisha foundation for the discovery and functional characterization ofbioactive peptides with pharmaceutical and pest-management potential.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":"25 11","pages":"5921–5934"},"PeriodicalIF":3.8,"publicationDate":"2026-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149330189","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