Journal of Proteome Research最新文献_第3页

Identification of FGG as a Biomarker in Early Gastric Cancer via Tissue Proteomics and Clinical Verification. 通过组织蛋白质组学和临床验证确定 FGG 作为早期胃癌的生物标记物

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-17 DOI: 10.1021/acs.jproteome.4c00624

Wujie Chen, Qihua Ye, Biying Zhang, Zhenhua Ma, Hanxiao Tu

{"title":"Identification of FGG as a Biomarker in Early Gastric Cancer via Tissue Proteomics and Clinical Verification.","authors":"Wujie Chen, Qihua Ye, Biying Zhang, Zhenhua Ma, Hanxiao Tu","doi":"10.1021/acs.jproteome.4c00624","DOIUrl":"10.1021/acs.jproteome.4c00624","url":null,"abstract":"Early and accurate diagnosis of gastric cancer (GC) is essential for reducing mortality and improving patient well-being. However, methods for the early diagnosis of GC are still lacking. In this study, by isobaric tagging for relative and absolute quantitation (iTRAQ), we identified 336 proteins that overlapped among the upregulated differentially expressed proteins (DEPs) in early gastric cancer (EGC) versus progressive gastric cancer (PGC), upregulated DEPs in EGC versus nongastric cancer (NGC), and nonsignificant proteins in EGC versus NGC. These DEPs were involved primarily in the neutrophil-related immune response. Network analysis of proteins and pathways revealed that fibrinogen α (FGA), β (FGB), and γ (FGG) are candidates for distinguishing EGC. Furthermore, parallel reaction monitoring (PRM), immunohistochemistry (IHC), and Western blot (WB) assays of clinical samples confirmed that, compared with that in PGC and NGC, only FGG was uniquely and significantly upregulated in the gastric mucosa of EGC. Our results demonstrated that FGG in the gastric mucosa could be a novel biomarker to diagnose EGC patients via endoscopy.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453388","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

Achieving a 35-Plex Tandem Mass Tag Reagent Set through Deuterium Incorporation. 通过氘结合实现 35 种串联质量标签试剂组合

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-09 DOI: 10.1021/acs.jproteome.4c00668

Nathan R Zuniga, Dustin C Frost, Karsten Kuhn, Myungsun Shin, Rebecca L Whitehouse, Ting-Yu Wei, Yuchen He, Shane L Dawson, Ian Pike, Ryan D Bomgarden, Steven P Gygi, Joao A Paulo

{"title":"Achieving a 35-Plex Tandem Mass Tag Reagent Set through Deuterium Incorporation.","authors":"Nathan R Zuniga, Dustin C Frost, Karsten Kuhn, Myungsun Shin, Rebecca L Whitehouse, Ting-Yu Wei, Yuchen He, Shane L Dawson, Ian Pike, Ryan D Bomgarden, Steven P Gygi, Joao A Paulo","doi":"10.1021/acs.jproteome.4c00668","DOIUrl":"10.1021/acs.jproteome.4c00668","url":null,"abstract":"Mass spectrometry-based sample multiplexing with isobaric tags permits the development of high-throughput and precise quantitative biological assays with proteome-wide coverage and minimal missing values. Here, we nearly doubled the multiplexing capability of the TMTpro reagent set to a 35-plex through the incorporation of one deuterium isotope into the reporter group. Substituting deuterium frequently results in suboptimal peak coelution, which can compromise the accuracy of reporter ion-based quantification. To counteract the deuterium effect on quantitation, we implemented a strategy that necessitated the segregation of nondeuterium and deuterium-containing channels into distinct subplexes during normalization procedures, with reassembly through a common bridge channel. This multiplexing strategy of \"design independent sub-plexes but acquire together\" (DISAT) was used to compare protein expression differences between human cell lines and in a cysteine-profiling (i.e., chemoproteomics) experiment to identify compounds binding to cysteine-113 of Pin1.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386403","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

Time-Resolved Multiomics Illustrates Host and Gut Microbe Interactions during Salmonella Infection. 时间分辨多组学图解沙门氏菌感染过程中宿主与肠道微生物的相互作用

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-07 DOI: 10.1021/acs.jproteome.4c00172

Yongseok Kim, Katherine Kokkinias, Anice Sabag-Daigle, Ikaia Leleiwi, Mikayla Borton, Michael Shaffer, Maryam Baniasad, Rebecca Daly, Brian M M Ahmer, Kelly C Wrighton, Vicki H Wysocki

{"title":"Time-Resolved Multiomics Illustrates Host and Gut Microbe Interactions during Salmonella Infection.","authors":"Yongseok Kim, Katherine Kokkinias, Anice Sabag-Daigle, Ikaia Leleiwi, Mikayla Borton, Michael Shaffer, Maryam Baniasad, Rebecca Daly, Brian M M Ahmer, Kelly C Wrighton, Vicki H Wysocki","doi":"10.1021/acs.jproteome.4c00172","DOIUrl":"10.1021/acs.jproteome.4c00172","url":null,"abstract":"Salmonella infection, also known as Salmonellosis, is one of the most common food-borne illnesses. Salmonella infection can trigger host defensive functions, including an inflammatory response. The provoked-host inflammatory response has a significant impact on the bacterial population in the gut. In addition, Salmonella competes with other gut microorganisms for survival and growth within the host. Compositional and functional alterations in gut bacteria occur because of the host immunological response and competition between Salmonella and the gut microbiome. Host variation and the inherent complexity of the gut microbial community make understanding commensal and pathogen interactions particularly difficult during a Salmonella infection. Here, we present metabolomics and lipidomics analyses along with the 16S rRNA sequence analysis, revealing a comprehensive view of the metabolic interactions between the host and gut microbiota during Salmonella infection in a CBA/J mouse model. We found that different metabolic pathways were altered over the four investigated time points of Salmonella infection (days -2, +2, +6, and +13). Furthermore, metatranscriptomics analysis integrated with metabolomics and lipidomics analysis facilitated an understanding of the heterogeneous response of mice, depending on the degree of dysbiosis.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142386409","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

LineageFilter: Improved Proteotyping of Complex Samples Using Metaproteomics and Machine Learning. LineageFilter：利用元蛋白质组学和机器学习改进复杂样本的蛋白质分型。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-19 DOI: 10.1021/acs.jproteome.4c00184

Hamid Hachemi, Jean Armengaud, Lucia Grenga, Olivier Pible

引用次数: 0

Defining Alzheimer's Disease through Proteomic CSF Profiling. 通过脑脊液蛋白质组分析确定阿尔茨海默氏症的病因

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-07 DOI: 10.1021/acs.jproteome.4c00590

Carmen Peña-Bautista, Lourdes Álvarez-Sánchez, Ángel Balaguer, Luis Raga, Lorena García-Vallés, Miguel Baquero, Consuelo Cháfer-Pericás

{"title":"Defining Alzheimer's Disease through Proteomic CSF Profiling.","authors":"Carmen Peña-Bautista, Lourdes Álvarez-Sánchez, Ángel Balaguer, Luis Raga, Lorena García-Vallés, Miguel Baquero, Consuelo Cháfer-Pericás","doi":"10.1021/acs.jproteome.4c00590","DOIUrl":"10.1021/acs.jproteome.4c00590","url":null,"abstract":"Alzheimer disease (AD) is the main cause of dementia, and its complexity is not yet completely understood. Proteomic profiles can provide useful information to explore the pathways involved and the heterogeneity among AD patients. A proteomic analysis was performed in cerebrospinal fluid (CSF) samples from mild cognitive impairment due to AD (MCI-AD) and control individuals; both groups were classified by amyloid β42/amyloid β40 levels in CSF (data available in BioStudies database (S-BSST1456)). The analysis based on PLS regression and volcano plot identified 7 proteins (FOLR2, PPP3CA, SMOC2, STMN1, TAGLN3, TMEM132B, and UCHL1) mainly related to protein phosphorylation, structure maintenance, inflammation, and protein degradation. Enrichment analysis revealed the involvement of different biological processes related to neuronal mechanisms and synapses, lipid and carbohydrate metabolism, immune system and inflammation, vascular, hormones, and response to stimuli, and cell signaling and adhesion. In addition, the proteomic profile showed some association with the levels of AD biomarkers in CSF. Regarding the subtypes, two MCI-AD subgroups were identified: one could be related to synapsis and neuronal functions and the other to innate immunity. The study of the proteomic profile in the CSF of AD patients reflects the heterogeneity of biochemical pathways involved in AD.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142379414","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

Multiomics Studies on Metabolism Changes in Alcohol-Associated Liver Disease. 酒精相关肝病代谢变化的多组学研究

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-17 DOI: 10.1021/acs.jproteome.4c00451

Liqing He, Raobo Xu, Xipeng Ma, Xinmin Yin, Eugene Mueller, Wenke Feng, Michael Menze, Seongho Kim, Craig J McClain, Xiang Zhang

{"title":"Multiomics Studies on Metabolism Changes in Alcohol-Associated Liver Disease.","authors":"Liqing He, Raobo Xu, Xipeng Ma, Xinmin Yin, Eugene Mueller, Wenke Feng, Michael Menze, Seongho Kim, Craig J McClain, Xiang Zhang","doi":"10.1021/acs.jproteome.4c00451","DOIUrl":"10.1021/acs.jproteome.4c00451","url":null,"abstract":"Metabolic dysfunction in the liver represents a predominant feature in the early stages of alcohol-associated liver disease (ALD). However, the mechanisms underlying this are only partially understood. To investigate the metabolic characteristics of the liver in ALD, we did a relative quantification of polar metabolites and lipids in the liver of mice with experimental ALD using untargeted metabolomics and untargeted lipidomics. A total of 99 polar metabolites had significant abundance alterations in the livers of alcohol-fed mice. Pathway analysis revealed that amino acid metabolism was the most affected by alcohol in the mouse liver. Metabolites involved in glycolysis and the TCA cycle were decreased, while glycerol 3-phosphate (G3P) and long-chain fatty acids were increased. Relative quantification of lipids unveiled an upregulation of multiple lipid classes, suggesting that alcohol consumption drives metabolism toward lipid synthesis. Results from enzyme expression and activity detection indicated that the decreased activity of mitochondrial glycerol 3-phosphate dehydrogenase contributed to the disordered metabolism.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453392","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

Meta-Analysis and DIA-MS-Based Proteomic Investigation of COPD Patients and Asymptomatic Smokers in the Indian Population. 对印度人群中的慢性阻塞性肺病患者和无症状吸烟者进行荟萃分析和基于 DIA-MS 的蛋白质组学研究。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-22 DOI: 10.1021/acs.jproteome.4c00463

Gautam Sharma, Debarghya Pratim Gupta, Koustav Ganguly, Mahesh Padukudru Anand, Sanjeeva Srivastava

{"title":"Meta-Analysis and DIA-MS-Based Proteomic Investigation of COPD Patients and Asymptomatic Smokers in the Indian Population.","authors":"Gautam Sharma, Debarghya Pratim Gupta, Koustav Ganguly, Mahesh Padukudru Anand, Sanjeeva Srivastava","doi":"10.1021/acs.jproteome.4c00463","DOIUrl":"10.1021/acs.jproteome.4c00463","url":null,"abstract":"Chronic obstructive pulmonary disease (COPD) is India's second largest cause of death and is largely caused by smoking. Asymptomatic smokers develop COPD due to genetic, environmental, and molecular variables, making early screening crucial. Data-independent acquisition mass spectrometry (DIA-MS) based-proteomics offers an unbiased method to analyze proteomic profiles. This study is the first to use DIA-based proteomics to analyze individual serum samples from three distinct male cohorts: healthy individuals (n = 10), asymptomatic smokers (n = 10), and COPD patients (n = 10). This comprehensive approach identified 667 proteins with a 1% false discovery rate. Differentially expressed proteins included 40 in the normal versus asymptomatic comparison, 88 in the COPD versus normal comparison, and 40 in the COPD versus asymptomatic comparison. Among them, protein-associated genes such as PRDX6, ELANE, PRKCSH, PRTN3, and MNDA could help differentiate COPD from asymptomatic smokers, while ELANE, H3-3A, IGHE, SLC4A1, and SERPINA11 could differentiate COPD from healthy subjects. Pathway enrichment and protein-protein interaction analyses revealed significant alterations in hemostasis, immune system functions, fibrin clot formation, and post-translational protein modifications. Key proteins were validated using a parallel reaction monitoring assay. DIA data are available via ProteomeXchange with identifier PXD055242. Our findings reveal key protein classifiers in COPD patients, asymptomatic smokers, and healthy individuals, helping clinicians understand disease pathobiology and improve disease management and quality of life.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491152","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

An Equine Protein Atlas Highlights Synovial Fluid Proteome Dynamics during Experimentally LPS-Induced Arthritis. 马蛋白质图谱突显了实验性 LPS 诱导关节炎期间滑膜液蛋白质组的动态变化。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-12 DOI: 10.1021/acs.jproteome.4c00125

Louise Bundgaard, Filip Årman, Emma Åhrman, Marie Walters, Ulrich Auf dem Keller, Johan Malmström, Stine Jacobsen

{"title":"An Equine Protein Atlas Highlights Synovial Fluid Proteome Dynamics during Experimentally LPS-Induced Arthritis.","authors":"Louise Bundgaard, Filip Årman, Emma Åhrman, Marie Walters, Ulrich Auf dem Keller, Johan Malmström, Stine Jacobsen","doi":"10.1021/acs.jproteome.4c00125","DOIUrl":"10.1021/acs.jproteome.4c00125","url":null,"abstract":"In human proteomics, substantial efforts are ongoing to leverage large collections of mass spectrometry (MS) fragment ion spectra into extensive spectral libraries (SL) as a resource for data independent acquisition (DIA) analysis. Currently, such initiatives in equine research are still missing. Here we present a large-scale equine SL, comprising 6394 canonical proteins and 89,329 unique peptides, based on data dependent acquisition analysis of 75 tissue and body fluid samples from horses. The SL enabled large-scale DIA-MS based quantification of the same samples to generate a quantitative equine protein distribution atlas to infer dominant proteins in different organs and body fluids. Data mining revealed 163 proteins uniquely identified in a specific type of tissue or body fluid, serving as a starting point to determine tissue-specific or tissue-type-specific proteins. We showcase the SL by highlighting proteome dynamics in equine synovial fluid samples during experimental lipopolysaccharide-induced arthritis. A fuzzy c-means cluster analysis pinpointed SERPINB1, ATRN, NGAL, LTF, MMP1, and LBP as putative biomarkers for joint inflammation. This SL provides an extendable resource for future equine studies employing DIA-MS.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536436/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142453372","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Detection and Quantification of Drug-Protein Adducts in Human Liver. 人体肝脏中药物蛋白加合物的检测与定量

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 Epub Date: 2024-10-23 DOI: 10.1021/acs.jproteome.4c00663

Alex Zelter, Michael Riffle, David D Shteynberg, Guo Zhong, Ellen B Riddle, Michael R Hoopmann, Daniel Jaschob, Robert L Moritz, Trisha N Davis, Michael J MacCoss, Nina Isoherranen

{"title":"Detection and Quantification of Drug-Protein Adducts in Human Liver.","authors":"Alex Zelter, Michael Riffle, David D Shteynberg, Guo Zhong, Ellen B Riddle, Michael R Hoopmann, Daniel Jaschob, Robert L Moritz, Trisha N Davis, Michael J MacCoss, Nina Isoherranen","doi":"10.1021/acs.jproteome.4c00663","DOIUrl":"10.1021/acs.jproteome.4c00663","url":null,"abstract":"Covalent protein adducts formed by drugs or their reactive metabolites are risk factors for adverse reactions, and inactivation of cytochrome P450 (CYP) enzymes. Characterization of drug-protein adducts is limited due to lack of methods identifying and quantifying covalent adducts in complex matrices. This study presents a workflow that combines data-dependent and data-independent acquisition (DDA and DIA) based liquid chromatography with tandem mass spectrometry (LC-MS/MS) to detect very low abundance adducts resulting from CYP mediated drug metabolism in human liver microsomes (HLMs). HLMs were incubated with raloxifene as a model compound and adducts were detected in 78 proteins, including CYP3A and CYP2C family enzymes. Experiments with recombinant CYP3A and CYP2C enzymes confirmed adduct formation in all CYPs tested, including CYPs not subject to time-dependent inhibition by raloxifene. These data suggest adducts can be benign. DIA analysis showed variable adduct abundance in many peptides between livers, but no concomitant decrease of unadducted peptides. This study sets a new standard for adduct detection in complex samples, offering insights into the human adductome resulting from reactive metabolite exposure. The methodology presented will aid mechanistic studies to identify, quantify and differentiate between adducts that result in adverse drug reactions and those that are benign.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142491148","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature. 蛋白质组学可以应对假基因编码性质的挑战。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-11-01 DOI: 10.1021/acs.jproteome.4c00116

Valeriia Vasylieva, Ihor Arefiev, Francis Bourassa, Félix-Antoine Trifiro, Marie A Brunet

引用次数: 0