Journal of Proteome Research最新文献

Lactyllysine Esterification Enables Efficient Lactylprotein Expression via Genetic Code Expansion and Supports Functional Proteomics Studies. 乳糖酸酯化可通过基因代码扩展实现乳糖蛋白的高效表达，并支持功能蛋白质组学研究。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-24 DOI: 10.1021/acs.jproteome.4c00525

Dexiang Wang, Chenguang Liu, Jingzhuo Chen, Yueyang Zhang, Rui Han, Shuo Tang, Nanxi Wang, Haiping Hao, Chang Shao, Hui Ye

{"title":"Lactyllysine Esterification Enables Efficient Lactylprotein Expression via Genetic Code Expansion and Supports Functional Proteomics Studies.","authors":"Dexiang Wang, Chenguang Liu, Jingzhuo Chen, Yueyang Zhang, Rui Han, Shuo Tang, Nanxi Wang, Haiping Hao, Chang Shao, Hui Ye","doi":"10.1021/acs.jproteome.4c00525","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00525","url":null,"abstract":"Lysine lactylation has recently been discovered and demonstrated to be an essential player in immunity, cancer and neurodegenerative diseases. Genetic code expansion (GCE) technique is powerful in uncovering lactylation functions, since it allows site-specific incorporation of lactyllysine (Klac) into proteins of interest (POIs) in living cells. However, the inefficient uptake of Klac into cells, due to its high hydrophilicity, results in limited expression of lactylated POIs. To address this challenge, here we designed esterified Klac derivatives, exemplified by ethylated Klac (KlacOEt), to enhance Klac's lipophilicity and improve its cellular uptake. The expression level of site-specifically lactylated POIs was doubled using KlacOEt in both Escherichia coli and HEK293T cells. Immunoprecipitation mass spectrometry analysis verified the significantly increased yield of the precisely lactylated fructose-bisphosphate aldolase A using KlacOEt. Furthermore, in conjunction with the Target Responsive Accessibility Profiling approach, we found that lactylation at ALDOA-K147 altered the protein's conformation, which may explain the lactylation-induced reduction in enzyme activity. Together, we demonstrate that, through enhancing the yield of lactylated proteins with Klac esters via GCE, we are able to site-specifically reveal the effects of lactylation on POIs' interactions, conformations and activities using a suite of functional proteomics and biochemical tools.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306588","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

Hydrophilic Interaction Chromatography Coupled to Ultraviolet Photodissociation Affords Identification, Localization, and Relative Quantitation of Glycans on Intact Glycoproteins. 亲水相互作用色谱法与紫外光解离技术可对完整糖蛋白上的聚糖进行鉴定、定位和相对定量。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-23 DOI: 10.1021/acs.jproteome.4c00600

Virginia K James, Annika A M van der Zon, Edwin E Escobar, Sean D Dunham, Andrea F G Gargano, Jennifer S Brodbelt

{"title":"Hydrophilic Interaction Chromatography Coupled to Ultraviolet Photodissociation Affords Identification, Localization, and Relative Quantitation of Glycans on Intact Glycoproteins.","authors":"Virginia K James, Annika A M van der Zon, Edwin E Escobar, Sean D Dunham, Andrea F G Gargano, Jennifer S Brodbelt","doi":"10.1021/acs.jproteome.4c00600","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00600","url":null,"abstract":"Protein glycosylation is implicated in a wide array of diseases, yet glycoprotein analysis remains elusive owing to the extreme heterogeneity of glycans, including microheterogeneity of some of the glycosites (amino acid residues). Various mass spectrometry (MS) strategies have proven tremendously successful for localizing and identifying glycans, typically utilizing a bottom-up workflow in which glycoproteins are digested to create glycopeptides to facilitate analysis. An emerging alternative is top-down MS that aims to characterize intact glycoproteins to allow precise identification and localization of glycans. The most comprehensive characterization of intact glycoproteins requires integration of a suitable separation method and high performance tandem mass spectrometry to provide both protein sequence information and glycosite localization. Here, we couple ultraviolet photodissociation and hydrophilic interaction chromatography with high resolution mass spectrometry to advance the characterization of intact glycoproteins ranging from 15 to 34 kDa, offering site localization of glycans, providing sequence coverages up to 93%, and affording relative quantitation of individual glycoforms.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306587","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

Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics. 利用工程纳米颗粒深入剖析血浆蛋白形式，实现自上而下的蛋白质组学。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-23 DOI: 10.1021/acs.jproteome.4c00621

Che-Fan Huang, Michael A Hollas, Aniel Sanchez, Mrittika Bhattacharya, Giang Ho, Ambika Sundaresan, Michael A Caldwell, Xiaoyan Zhao, Ryan Benz, Asim Siddiqui, Neil L Kelleher

{"title":"Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-Down Proteomics.","authors":"Che-Fan Huang, Michael A Hollas, Aniel Sanchez, Mrittika Bhattacharya, Giang Ho, Ambika Sundaresan, Michael A Caldwell, Xiaoyan Zhao, Ryan Benz, Asim Siddiqui, Neil L Kelleher","doi":"10.1021/acs.jproteome.4c00621","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00621","url":null,"abstract":"The dynamic range challenge for the detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundance proteins selectively and reproducibly from human plasma and use top-down proteomics to quantify differential enrichment for the 2841 detected proteoforms from 114 proteins. Furthermore, nanoparticle enrichment allowed top-down detection of proteoforms between ∼1 μg/mL and ∼10 pg/mL in absolute abundance, providing up to a 105-fold increase in proteome depth over neat plasma in which only proteoforms from abundant proteins (>1 μg/mL) were detected. The ability to monitor medium and some low-abundant proteoforms through reproducible enrichment significantly extends the applicability of proteoform research by adding depth beyond albumin, immunoglobins, and apolipoproteins to uncover many involved in immunity and cell signaling. As proteoforms carry unique information content relative to peptides, this report opens the door to deeper proteoform sequencing in clinical proteomics of disease or aging cohorts.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306586","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

Rps3 Attenuates Gastric Precancerous Lesions by Promoting Dendritic Cells Maturation via AKT/β-Catenin Pathway. Rps3通过AKT/β-Catenin通路促进树突状细胞成熟从而减轻胃癌前病变

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-22 DOI: 10.1021/acs.jproteome.4c00472

Siyi Li, Bijuan Xiao, Yuting Zhan, Zhulin Wu, Weiqing Zhang, Huafeng Pan, Weijun Luo

{"title":"Rps3 Attenuates Gastric Precancerous Lesions by Promoting Dendritic Cells Maturation via AKT/β-Catenin Pathway.","authors":"Siyi Li, Bijuan Xiao, Yuting Zhan, Zhulin Wu, Weiqing Zhang, Huafeng Pan, Weijun Luo","doi":"10.1021/acs.jproteome.4c00472","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00472","url":null,"abstract":"This study aimed to investigate the dysregulated proteins and the underlying mechanisms of gastric precancerous lesions. Proteomic and phosphoproteomic methods were used to characterize the proteome and phosphoproteome profiles of N-methyl-N-nitro-N-nitrosoguanidine (MNNG)-induced gastric precancerous lesions. The hub differentially expressed proteins (DEPs) and phosphoproteins (DEPPs) were identified by using differential expression and protein-protein interaction network analyses. Western blot assay, quantitative reverse transcription (qRT)-PCR, and CCK-8 assays detected the expression of Rps3, N-cadherin, E-cadherin, AKT, p-AKT, and β-catenin and verified the roles of Rps3 on the MNNG-induced human gastric epithelial cell line (GES-1) cells. Hub DEPs and phosphoproteins Rps3, Akt1, and Ctnnb1 were significantly correlated with five dendritic cells (DCs) pathways, and Akt1 and Ctnnb1 were significantly negatively correlated with Rps3. MNNG administration markedly reduced the Rps3 mRNA and protein expression levels (all P < 0.05). Overexpression of Rps3 significantly inhibited tumorigenesis of MNNG-induced GES-1 cells (all P < 0.01) and changed the protein levels of N-cadherin, E-cadherin, AKT, p-AKT, and β-catenin. Similarly, SC79 treatment substantially increased the expression of interleukin (IL)-6, IL-10, and vascular endothelial growth factor (all P < 0.05). Rps3 was poorly expressed in precancerous gastric lesions. Correspondingly, overexpression of Rps3 promoted DC maturation via the AKT/β-catenin pathway, inhibiting the progression of gastric precancerous lesions.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277343","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

Reliability of Serum-Derived Connectome Indicators in Identifying Cirrhosis. 血清生成的连接组指标在鉴别肝硬化中的可靠性

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-21 DOI: 10.1021/acs.jproteome.4c00699

Jisheng Guo, Xiaona Wang, Guangming Li, Qiong Wang, Fengqin Wang, Jinjin Liu, Xu Feng, Chao Wang

{"title":"Reliability of Serum-Derived Connectome Indicators in Identifying Cirrhosis.","authors":"Jisheng Guo, Xiaona Wang, Guangming Li, Qiong Wang, Fengqin Wang, Jinjin Liu, Xu Feng, Chao Wang","doi":"10.1021/acs.jproteome.4c00699","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00699","url":null,"abstract":"Patients with cirrhosis face a heightened risk of complications, underscoring the importance of identification. We have developed a Connectome strategy that combines metabolites with peptide spectral matching (PSM) in proteomics to integrate metabolomics and proteomics, identifying specific metabolites bound to blood proteins in cirrhosis using open search proteomics methods. Analysis methods including Partial Least Squares Discriminant Analysis (PLS-DA), Uniform Manifold Approximation and Projection (UMAP), and hierarchical clustering were used to distinguish significant differences among the Cirrhosis group, Chronic Hepatitis B (CHB) group, and Healthy group. In this study, we identified 81 cirrhosis-associated connectomes and established an effective model distinctly distinguishing cirrhosis from chronic hepatitis B and healthy samples, confirmed by PLS-DA, hierarchical clustering analysis, and UMAP analysis, and further validated using six new cirrhosis samples. We established a Unified Indicator for Identifying cirrhosis, including tyrosine, Unnamed_189.2, thiazolidine, etc., which not only enables accurate identification of cirrhosis groups but was also further validated using six new cirrhosis samples and extensively supported by other cirrhosis research data (PXD035024). Our study reveals that characteristic cirrhosis connectomes can reliably distinguish cirrhosis from CHB and healthy groups. The established unified cirrhotic indicator facilitates the identification of cirrhosis cases in both this study and additional research data.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277342","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

Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics 系统评估用于 O-谷氨酰核糖蛋白质组学的亲和富集方法

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-20 DOI: 10.1021/acs.jproteome.4c00388

Chunyan Hou, Ci Wu, Zichun Wu, Yifan Cheng, Weiyu Li, Hui Sun, Junfeng Ma

{"title":"Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics","authors":"Chunyan Hou, Ci Wu, Zichun Wu, Yifan Cheng, Weiyu Li, Hui Sun, Junfeng Ma","doi":"10.1021/acs.jproteome.4c00388","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00388","url":null,"abstract":"O-Linked β-N-acetylglucosamine (O-GlcNAc) modification (i.e., O-GlcNAcylation) on proteins plays critical roles in the regulation of diverse biological processes. However, protein O-GlcNAcylation analysis, especially at a large scale, has been a challenge. So far, a number of enrichment materials and methods have been developed for site-specific O-GlcNAc proteomics in different biological settings. Despite the presence of multiple methods, their performance for the O-GlcNAc proteomics is largely unclear. In this work, by using the lysates of PANC-1 cells (a pancreatic cancer cell line), we provided a head-to-head comparison of three affinity enrichment methods and materials (i.e., antibody, lectin AANL6, and an OGA mutant) for site-specific O-GlcNAc proteomics. The enriched peptides were analyzed by HCD product-dependent EThcD (i.e., HCD-pd-EThcD) mass spectrometry. The resulting data files were processed by three different data analysis packages (i.e., Sequest HT, Byonic, and FragPipe). Our data suggest that each method captures a subpopulation of the O-GlcNAc proteins. Besides the enrichment methods, we also observe complementarity between the different data analysis tools. Thus, combining different approaches holds promise for enhanced coverage of O-GlcNAc proteomics.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264720","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

Functional and Proteomic Dissection of the Contributions of CodY, SigB and the Hibernation Promoting Factor HPF to Interactions of Staphylococcus aureus USA300 with Human Lung Epithelial Cells. 从功能和蛋白质组学角度剖析 CodY、SigB 和冬眠促进因子 HPF 对金黄色葡萄球菌 USA300 与人类肺上皮细胞相互作用的贡献。

IF 3.8 2区生物学

Journal of Proteome Research Pub Date : 2024-09-20 DOI: 10.1021/acs.jproteome.4c00724

Xiaofang Li, Larissa M Busch, Sjouke Piersma, Min Wang, Lei Liu, Manuela Gesell Salazar, Kristin Surmann, Ulrike Mäder, Uwe Völker, Girbe Buist, Jan Maarten van Dijl

{"title":"Functional and Proteomic Dissection of the Contributions of CodY, SigB and the Hibernation Promoting Factor HPF to Interactions of Staphylococcus aureus USA300 with Human Lung Epithelial Cells.","authors":"Xiaofang Li, Larissa M Busch, Sjouke Piersma, Min Wang, Lei Liu, Manuela Gesell Salazar, Kristin Surmann, Ulrike Mäder, Uwe Völker, Girbe Buist, Jan Maarten van Dijl","doi":"10.1021/acs.jproteome.4c00724","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00724","url":null,"abstract":"Staphylococcus aureus is a leading cause of severe pneumonia. Our recent proteomic investigations into S. aureus invasion of human lung epithelial cells revealed three key adaptive responses: activation of the SigB and CodY regulons and upregulation of the hibernation-promoting factor SaHPF. Therefore, our present study aimed at a functional and proteomic dissection of the contributions of CodY, SigB and SaHPF to host invasion using transposon mutants of the methicillin-resistant S. aureus USA300. Interestingly, disruption of codY resulted in a \"small colony variant\" phenotype and redirected the bacteria from (phago)lysosomes into the host cell cytoplasm. Furthermore, we show that CodY, SigB and SaHPF contribute differentially to host cell adhesion, invasion, intracellular survival and cytotoxicity. CodY- or SigB-deficient bacteria experienced faster intracellular clearance than the parental strain, underscoring the importance of these regulators for intracellular persistence. We also show an unprecedented role of SaHPF in host cell adhesion and invasion. Proteomic analysis of the different mutants focuses attention on the CodY-perceived metabolic state of the bacteria and the SigB-perceived environmental cues in bacterial decision-making prior and during infection. Additionally, it underscores the impact of the nutritional status and bacterial stress on the initiation and progression of staphylococcal lung infections.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142277341","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

Proteomic and Phosphoproteomic Profiling of Matrix Stiffness-Induced Stemness-Dormancy State Transition in Breast Cancer Cells 基质僵化诱导乳腺癌细胞干性-休眠状态转变的蛋白质组和磷酸蛋白组分析

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-19 DOI: 10.1021/acs.jproteome.4c00563

Rong Han, Xu Sun, Yue Wu, Ye-Hong Yang, Qiao-Chu Wang, Xu-Tong Zhang, Tao Ding, Jun-Tao Yang

{"title":"Proteomic and Phosphoproteomic Profiling of Matrix Stiffness-Induced Stemness-Dormancy State Transition in Breast Cancer Cells","authors":"Rong Han, Xu Sun, Yue Wu, Ye-Hong Yang, Qiao-Chu Wang, Xu-Tong Zhang, Tao Ding, Jun-Tao Yang","doi":"10.1021/acs.jproteome.4c00563","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00563","url":null,"abstract":"The dormancy of cancer stem cells is a major factor leading to drug resistance and a high rate of late recurrence and mortality in estrogen receptor-positive (ER+) breast cancer. Previously, we demonstrated that a stiffer matrix induces tumor cell dormancy and drug resistance, whereas a softened matrix promotes tumor cells to exhibit a stem cell state with high proliferation and migration. In this study, we present a comprehensive analysis of the proteome and phosphoproteome in response to gradient changes in matrix stiffness, elucidating the mechanisms behind cell dormancy-induced drug resistance. Overall, we found that antiapoptotic and membrane transport processes may be involved in the mechanical force-induced dormancy resistance of ER+ breast cancer cells. Our research provides new insights from a holistic proteomic and phosphoproteomic perspective, underscoring the significant role of mechanical forces stemming from the stiffness of the surrounding extracellular matrix as a critical regulatory factor in the tumor microenvironment.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264725","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

Analysis of Brain Protein Stability Changes in a Mouse Model of Alzheimer’s Disease 阿尔茨海默病小鼠模型脑蛋白稳定性变化分析

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-18 DOI: 10.1021/acs.jproteome.4c00406

Yun Tang, Hye-Jin Park, Shengyu Li, Michael C. Fitzgerald

{"title":"Analysis of Brain Protein Stability Changes in a Mouse Model of Alzheimer’s Disease","authors":"Yun Tang, Hye-Jin Park, Shengyu Li, Michael C. Fitzgerald","doi":"10.1021/acs.jproteome.4c00406","DOIUrl":"https://doi.org/10.1021/acs.jproteome.4c00406","url":null,"abstract":"The stability of proteins from rates of oxidation (SPROX), thermal proteome profiling (TPP), and limited proteolysis (LiP) techniques were used to profile the stability of ∼2500 proteins in hippocampus tissue cell lysates from 2- and 8-months-old wild-type (C57BL/6J; n = 7) and transgenic (5XFAD; n = 7) mice with five Alzheimer’s disease (AD)-linked mutations. Approximately 200–500 protein hits with AD-related stability changes were detected by each technique at each age point. The hit overlap from technique to technique was low, and all of the techniques generated protein hits that were more numerous and largely different from those identified in protein expression level analyses, which were also performed here. The hit proteins identified by each technique were enriched in a number of the same pathways and biological processes, many with known connections to AD. The protein stability hits included 25 high-value conformation biomarkers with AD-related stability changes detected using at least 2 techniques at both age points. Also discovered were subunit- and age-specific AD-related stability changes in the proteasome, which had reduced function at both age points. The different folding stability profiles of the proteasome at the two age points are consistent with a different mechanism for proteasome dysfunction at the early and late stages of AD.","PeriodicalId":48,"journal":{"name":"Journal of Proteome Research","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264721","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

Revisiting Protein Reversed-Phase Chromatography for Bottom-Up Proteomics 重新审视蛋白质反相色谱法在自下而上蛋白质组学中的应用

IF 4.4 2区生物学

Journal of Proteome Research Pub Date : 2024-09-18 DOI: 10.1021/acs.jproteome.4c00642

Shunsuke Takagi, Nobuyuki Suzuki, Yasushi Ishihama

引用次数: 0