Proteomics最新文献

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Psidium Defenses Against Meloidogyne enterolobii: Proteomic and Microscopic Analysis of this Plant-Predator Association 蕨类植物-掠食性植物协会的蛋白质组学和显微分析。

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-26 DOI: 10.1002/pmic.70015

Sara Nállia de Oliveira Costa, Roberta Pena da Paschoa, Camilla Ribeiro Alexandrino, Pamela Maciel Cremonez, Juliana Martins Ribeiro, José Mauro da Cunha e Castro, Maura Da Cunha, Vanildo Silveira, Antônia Elenir Amâncio Oliveira, Kátia Valevski Sales Fernandes

Guava (Psidium guajava), referred to as the “tropical apple,” is esteemed for its sweet flavor, nutritional density, and medicinal attributes, being rich in ascorbic acid, phenolics, carotenoids, fibers, and minerals. Despite its agricultural significance, guava cultivation faces considerable challenges from plant-parasitic nematodes, particularly root-knot nematodes from the Meloidogyne spp. In South America, Meloidogyne enterolobii causes severe root damage and economic losses to this crop. Plants fight nematodes through complex immune mechanisms involving pattern recognition receptors and signaling pathways, such as pattern-triggered immunity. The present research employed comparative shotgun proteomic analysis complemented by microscopic imaging and histochemical assays of roots from susceptible P. guajava and resistant P. guineense, inoculated or not with M. enterolobii. Psidium-M. enterolobii interactions revealed intricate plant cellular responses such as giant cells formation, hypersensitivity reactions, and biochemical pathway adjustments in sucrose transport and antioxidant enzyme activities. Synthesis and accumulation of secondary metabolites like terpenes, alkaloids, and phenolics in inoculated and resistant plants were positively correlated to plant resilience. Heat shock proteins and protein disulfide isomerases also emerged as pivotal in plant response, being upregulated during nematode infection.

Summary

The work addresses and unravels some of the puzzle pieces in the net of processes triggered in a plant prey (Psidium spp.), of either susceptible (P. guajava) or resistant (P. guineense) phenotypes, when confronted by its nematode predator (Meloidogyne enterolobii).
The main alterations detected in the roots of these plants ranged from giant cells formation, hypersensitivity reactions, biochemical adjustments in sucrose transport pathways and in antioxidant enzyme activities, to increases in secondary metabolites (terpenes, alkaloids, and phenolics) and in heat shock proteins and protein disulfide isomerases.
All these defensive mechanisms were triggered by the nematode attack on both species and were more prominent in P. guineense, which positively correlates them to the plant resistance against M. enterolobii.

番石榴（Psidium guajava），被称为“热带苹果”，因其甜味、营养密度和药用特性而备受推崇，富含抗坏血酸、酚类物质、类胡萝卜素、纤维和矿物质。尽管番石榴具有重要的农业意义，但番石榴种植面临着来自植物寄生线虫的巨大挑战，特别是来自Meloidogyne spp的根结线虫。在南美洲，Meloidogyne enterolobii给番石榴作物造成严重的根系损害和经济损失。植物通过复杂的免疫机制对抗线虫，包括模式识别受体和信号通路，如模式触发免疫。本研究采用比较霰弹枪蛋白质组学分析，辅以显微镜成像和组织化学分析，对接种或未接种肠肠杆菌的瓜石榴易感和抗性豚鼠弓形虫的根进行分析。Psidium-M。肠弧菌的相互作用揭示了复杂的植物细胞反应，如巨细胞形成、超敏反应和蔗糖运输和抗氧化酶活性的生化途径调节。接种和抗性植株次生代谢产物萜类、生物碱和酚类物质的合成和积累与植株抗逆性呈正相关。热休克蛋白和蛋白二硫异构酶也在植物反应中起关键作用，在线虫感染期间被上调。摘要：这项工作解决并解开了植物猎物（Psidium spp.）在面对其线虫捕食者（Meloidogyne enterolobii）时触发的过程中的一些难题，这些过程可能是易感的（P. guajava）或抗性的（P. guineense）表型。在这些植物的根中检测到的主要变化包括巨细胞形成、超敏反应、蔗糖运输途径和抗氧化酶活性的生化调整、次生代谢物（萜烯、生物碱和酚类物质）以及热休克蛋白和蛋白二硫异构酶的增加。所有这些防御机制都是由线虫对这两个物种的攻击触发的，并且在几内亚假单胞虫中更为突出，这与植物对肠梭菌的抗性呈正相关。

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引用次数: 0

Enhanced Separation of Intact Proteins and Proteoforms by CZE-MS Using Sulfobetaine-Modified Poly(α-L-lysine)-Based Multilayer Coatings for EOF Adjustment 巯基甜菜碱修饰聚α- l -赖氨酸多层膜的EOF调节增强了CZE-MS对完整蛋白和蛋白形态的分离

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-25 DOI: 10.1002/pmic.70012

Alisa Höchsmann, Henry Frick, Laura Dhellemmes, Laurent Leclercq, Philipp T. Kaulich, Andreas Tholey, Hervé Cottet, Norbert Schaschke, Christian Neusüß

Mass spectrometry–based top-down protein analysis requires efficient separation. In the context of proteoform analysis, capillary zone electrophoresis (CZE) is very valuable. The resolution of two peaks in CZE can be increased when the absolute mobility of the counter-directed electroosmotic flow (EOF) is close to the effective mobility of the analytes, resulting in a low apparent mobility of the analytes. The mobility of the EOF of highly efficient sulfobetaine-modified poly(α-L-lysine) (α-PLL) coatings changes depending on the number of modified side chains. Here, such coatings are used to selectively increase the peak resolution of proteoforms of model proteins and analytes in a complex protein sample (intact yeast protein extract). Whereas a high EOF system allows for the separation of proteins of a wide mobility range (complete proteome), lower EOF systems allow for a much better separation of proteins and proteoforms of low mobility, including those containing acidic post-translation modifications (PTMs). This leads to the identification of 2.5 times more proteoforms by MS/MS experiments in the lower mobility range of the yeast proteome. The sulfobetaine-modified α-PLL coatings presented here exhibit a toolbox for highly resolved separation of proteins and proteoforms in targeted or untargeted top-down protein analysis.

Summary

Sample complexity is one of the main challenges when analyzing a proteome on the proteoform level.
In the course of this, capillary electrophoresis–mass spectrometry turned out to be an excellent tool because of its high-performing separation, particularly for large molecules.
Here, we present a method enabling the best possible separation due to efficient and EOF-tunable coatings, allowing for flexible and dedicated selection of a range of proteins and proteoforms to be analyzed under ideal separation conditions.
The high performance is demonstrated by the separation of proteoforms of common PTM-rich model proteins as well as complex proteome samples.

基于质谱的自上而下的蛋白质分析需要有效的分离。在蛋白质分析中，毛细管区带电泳（CZE）具有重要的应用价值。当反定向电渗透流（EOF）的绝对迁移率接近分析物的有效迁移率时，CZE中两个峰的分辨率可以提高，导致分析物的表观迁移率较低。高效磺胺甜菜碱修饰聚α- l -赖氨酸（α-PLL）涂层的EOF迁移率随修饰侧链数量的变化而变化。在这里，这种涂层被用来选择性地增加复杂蛋白质样品（完整的酵母蛋白提取物）中模型蛋白质和分析物的蛋白质形态的峰值分辨率。高EOF系统允许宽迁移范围的蛋白质（完整的蛋白质组）的分离，而低EOF系统允许低迁移率的蛋白质和蛋白质形式的更好的分离，包括那些含有酸性翻译后修饰（PTMs）的蛋白质。这使得在酵母蛋白质组的低迁移率范围内，通过MS/MS实验鉴定出的蛋白质形态增加了2.5倍。本文提出的磺胺甜菜碱修饰的α-PLL涂层在靶向或非靶向自上而下的蛋白质分析中具有高分辨率的蛋白质和蛋白质形态分离工具箱。摘要：样品复杂性是分析蛋白质组在蛋白质形态水平上的主要挑战之一。在此过程中，毛细管电泳-质谱法被证明是一种极好的工具，因为它具有高性能的分离，特别是对于大分子。在这里，我们提出了一种方法，由于高效和eof可调的涂层，可以实现最佳的分离，允许在理想的分离条件下灵活和专用地选择一系列蛋白质和蛋白质形态进行分析。通过对常见的富含ptm的模型蛋白和复杂蛋白质组样品的蛋白质形态的分离，证明了该方法的高性能。

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引用次数: 0

Extracellular Origins of Cognition: Lessons from Primate Neocortical ECM 认知的细胞外起源：来自灵长类动物新皮层ECM的教训

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-22 DOI: 10.1002/pmic.13979

Shani Stern

The brain's extracellular matrix (ECM) is an intricate and dynamic network that plays essential roles in neurodevelopment, synaptic plasticity, and circuit stability. Despite its importance, the molecular composition and spatial organization of the developing brain ECM remain poorly characterized. In this commentary, we highlight the recent study by Vilicich et al., which employs a multi-modal approach, integrating single-cell transcriptomics, proteomics, and immunohistofluorescence, to construct a map of the ECM in the developing neocortex of humans and non-human primates. By curating a comprehensive list of extracellular proteins termed the “Exomatrix” and analyzing their distribution across cortical layers and developmental stages, the authors reveal layer-specific and evolutionarily conserved ECM features. These findings not only expand our understanding of ECM's role in shaping the brain during early development but also emphasize its potential involvement in the pathogenesis of neurodevelopmental disorders, urging further research into ECM biology as a frontier in neuroscience.

脑细胞外基质（ECM）是一个复杂的动态网络，在神经发育、突触可塑性和回路稳定性中起着重要作用。尽管其重要性，发育中的脑ECM的分子组成和空间组织仍然缺乏表征。在这篇评论中，我们重点介绍了Vilicich等人最近的一项研究，该研究采用多模式方法，整合单细胞转录组学、蛋白质组学和免疫组织荧光，构建了人类和非人类灵长类动物发育中的新皮层的ECM图谱。通过整理被称为“Exomatrix”的细胞外蛋白的综合列表，并分析它们在皮层层和发育阶段的分布，作者揭示了层特异性和进化保守的ECM特征。这些发现不仅扩大了我们对ECM在早期发育过程中塑造大脑的作用的理解，而且强调了它在神经发育障碍发病机制中的潜在参与，促使进一步研究ECM生物学作为神经科学的前沿。

引用次数: 0

Issue Information: Proteomics 14'25 出版信息：蛋白质组学14'25

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-22 DOI: 10.1002/pmic.70021

引用次数: 0

An INS-1 832/13 𝛽-Cell Proteome Highlights the Rapid Regulation of Fatty Acid Biosynthesis in Glucose-Stimulated Insulin Secretion INS-1 832/13𝛽-Cell蛋白质组强调了脂肪酸生物合成在葡萄糖刺激胰岛素分泌中的快速调节。

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-20 DOI: 10.1002/pmic.70005

Nina Stremmel, Oliver Lemke, Kathrin Textoris-Taube, Daniela Ludwig, Michael Mülleder, Julia Muenzner, Markus Ralser

Pancreatic beta cells secrete insulin in response to rising glucose levels, a process known as glucose-stimulated insulin secretion (GSIS). Here, we acquire proteomes of rat pancreatic INS-1 832/13 beta cells that were short-term stimulated with 11 different glucose concentrations from 0 to 20 mM, quantifying the response of 3703 proteins. Ensemble clustering of proteome profiles revealed unique response patterns of proteins expressed by INS-1 832/13 cells. Three hundred and fourteen proteins, amongst them proteins associated with vesicular SNARE interactions, protein export, and pancreatic secretion, increased in abundance upon glucose stimulation. In contrast, many proteins implicated in metabolic glucose sensing processes such as glycolysis, the TCA cycle, and the respiratory chain, did not respond. Interestingly, we observe that enzymes participating in fatty acid metabolism showed a “switch-on” response upon release of complete glucose starvation with no further changes in abundance upon increasing glucose levels. We speculate that increased activity of fatty acid metabolic activity might either be part of GSIS by replenishing membrane lipids required for vesicle-mediated exocytosis and/or by providing an electron sink to compensate for the increase in glucose catabolism. These findings offer new insights into beta cell function and may inform future strategies for targeting metabolic pathways in diabetes treatment.

Summary

We used high-throughput proteomics to capture comprehensive proteome changes 30 min post stimulation in the INS-1 832/13 beta cell line, a commonly used cell model in studying glucose-induced insulin secretion.
Our results show that specific parts of the proteome respond promptly upon glucose exposure in this cell line. Furthermore, while many proteins canonically associated with GSIS did not change in abundance in the time frame and cell line investigated, our results attribute a specific role to fatty acid biosynthesis in the early steps of insulin secretion.
By documenting protein abundance alterations in the initial phase of GSIS in the INS-1 832/13 beta cell line, our study highlights the necessity of sampling early time points, well-controlled study design and biological replicates in the study of beta cell function.

胰腺细胞分泌胰岛素以应对葡萄糖水平的升高，这一过程被称为葡萄糖刺激胰岛素分泌（GSIS）。在这里，我们获得了大鼠胰腺ins - 1832 /13 β细胞的蛋白质组，这些细胞在0到20 mM的11种不同葡萄糖浓度下短期刺激，量化了3703种蛋白质的反应。蛋白质组谱的集合聚类揭示了ins - 1832 /13细胞表达的蛋白质的独特响应模式。在葡萄糖刺激下，314种蛋白质（其中包括与水疱SNARE相互作用、蛋白质输出和胰腺分泌相关的蛋白质）的丰度增加。相反，许多与代谢葡萄糖感知过程有关的蛋白质，如糖酵解、TCA循环和呼吸链，没有反应。有趣的是，我们观察到参与脂肪酸代谢的酶在完全葡萄糖饥饿释放时表现出“开启”反应，而在葡萄糖水平升高时没有进一步的变化。我们推测脂肪酸代谢活性的增加可能是GSIS的一部分，通过补充囊泡介导的胞外分泌所需的膜脂和/或通过提供电子汇来补偿葡萄糖分解代谢的增加。这些发现为β细胞功能提供了新的见解，并可能为未来糖尿病治疗中针对代谢途径的策略提供信息。摘要：我们使用高通量蛋白质组学技术捕获了INS-1 832/13 β细胞系（研究葡萄糖诱导胰岛素分泌的常用细胞模型）刺激后30分钟的全面蛋白质组变化。我们的研究结果表明，在这种细胞系中，蛋白质组的特定部分对葡萄糖暴露迅速作出反应。此外，虽然许多通常与GSIS相关的蛋白质在研究的时间框架和细胞系中丰度没有变化，但我们的研究结果将脂肪酸在胰岛素分泌的早期阶段的生物合成归因于特定的作用。通过记录INS-1 832/13 β细胞系GSIS初始阶段蛋白丰度的变化，我们的研究强调了在β细胞功能研究中取样早期时间点、良好控制的研究设计和生物重复的必要性。

{"title":"An INS-1 832/13 𝛽-Cell Proteome Highlights the Rapid Regulation of Fatty Acid Biosynthesis in Glucose-Stimulated Insulin Secretion","authors":"Nina Stremmel, Oliver Lemke, Kathrin Textoris-Taube, Daniela Ludwig, Michael Mülleder, Julia Muenzner, Markus Ralser","doi":"10.1002/pmic.70005","DOIUrl":"10.1002/pmic.70005","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>Pancreatic beta cells secrete insulin in response to rising glucose levels, a process known as glucose-stimulated insulin secretion (GSIS). Here, we acquire proteomes of rat pancreatic INS-1 832/13 beta cells that were short-term stimulated with 11 different glucose concentrations from 0 to 20 mM, quantifying the response of 3703 proteins. Ensemble clustering of proteome profiles revealed unique response patterns of proteins expressed by INS-1 832/13 cells. Three hundred and fourteen proteins, amongst them proteins associated with vesicular SNARE interactions, protein export, and pancreatic secretion, increased in abundance upon glucose stimulation. In contrast, many proteins implicated in metabolic glucose sensing processes such as glycolysis, the TCA cycle, and the respiratory chain, did not respond. Interestingly, we observe that enzymes participating in fatty acid metabolism showed a “switch-on” response upon release of complete glucose starvation with no further changes in abundance upon increasing glucose levels. We speculate that increased activity of fatty acid metabolic activity might either be part of GSIS by replenishing membrane lipids required for vesicle-mediated exocytosis and/or by providing an electron sink to compensate for the increase in glucose catabolism. These findings offer new insights into beta cell function and may inform future strategies for targeting metabolic pathways in diabetes treatment.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Summary</h3>\u0000 \u0000 <div>\u0000 <ul>\u0000 \u0000 <li>We used high-throughput proteomics to capture comprehensive proteome changes 30 min post stimulation in the INS-1 832/13 beta cell line, a commonly used cell model in studying glucose-induced insulin secretion.</li>\u0000 \u0000 <li>Our results show that specific parts of the proteome respond promptly upon glucose exposure in this cell line. Furthermore, while many proteins canonically associated with GSIS did not change in abundance in the time frame and cell line investigated, our results attribute a specific role to fatty acid biosynthesis in the early steps of insulin secretion.</li>\u0000 \u0000 <li>By documenting protein abundance alterations in the initial phase of GSIS in the INS-1 832/13 beta cell line, our study highlights the necessity of sampling early time points, well-controlled study design and biological replicates in the study of beta cell function.</li>\u0000 </ul>\u0000 </div>\u0000 </section>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"25 15","pages":"13-26"},"PeriodicalIF":3.9,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12332333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144673545","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

LC-MS/MS Characterization of SOBERANA 02, a Receptor Binding Domain-Tetanus Toxoid Conjugate Vaccine Against SARS-CoV-2 抗SARS-CoV-2受体结合域-破伤风类毒素结合疫苗SOBERANA 02的LC-MS/MS鉴定

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-18 DOI: 10.1002/pmic.13978

Olivia Martínez, Darielys Santana-Medero, Satomy Pousa, Jean Pierre Soubal, Arielis Rodríguez-Ulloa, Pablo E. Ramos-Bermúdez, Vladimir Besada, Raine Garrido, Paulo Carvalho, Michel Batista, Katharina Zetl, Jacek R. Wiśniewski, Tamy Boggiano, Yury Valdés-Balbín, Dagmar García-Rivera, Daniel G. Rivera, Vicente Verez-Bencomo, Luis Javier González

SOBERANA 02 is a safe and effective anti-SARS-CoV-2 conjugate vaccine, produced using the maleimide-thiol chemistry. In this vaccine, Cys⁵³⁸ in the recombinant receptor binding domain (RBD) of SARS-CoV-2 is linked through a N-thiosuccinimidopropionyl linker to lysine residues of tetanus toxoid (TT) preparation. LC-MS/MS analysis revealed the complex protein composition of TT. The fifteen most abundant proteins account for approximately 78% of the total protein mass. The detoxified tetanus neurotoxin (d-TeNT) was the most abundant protein (30%–56%) regardless of the quantification method used. LC-MS/MS analysis of d-TeNT activation reaction with BMPS (3-maleimidopropionic acid N-hydroxysuccinimide ester) showed that 102 (95%) of the 107 lysine residues incorporated a maleimide group. Of them, only 22 Lys residues (20%) were cross-linked to the RBD C-terminal tryptic peptide (⁵³⁸CVNF⁵⁴¹-HHHHHH), probably due to steric hindrance. Affinity chromatography prior to LC-MS/MS analysis was critical to identify the conjugation sites. Linear peptides carrying a conjugated lysine residue and type 2 peptides with stabilized linker forms (hydrolyzed and transcyclized), allowed the identification of twelve and eighteen conjugation sites, respectively. The RBD was also conjugated, but to a lesser extent, to ten other low-abundance carrier proteins. This study represents the first report of a conjugation site assignment in a TT-based conjugate vaccine.

SOBERANA 02是一种安全有效的抗sars - cov -2结合疫苗，使用马来酰亚胺-硫醇化学生产。在该疫苗中，SARS-CoV-2重组受体结合域（RBD）中的Cys538通过n -硫代琥珀酰亚胺丙酰连接到破伤风类毒素（TT）制剂的赖氨酸残基上。LC-MS/MS分析显示了TT的复杂蛋白组成。最丰富的15种蛋白质约占总蛋白质质量的78%。无论采用何种定量方法，解毒破伤风神经毒素（d-TeNT）都是最丰富的蛋白质（30%-56%）。LC-MS/MS分析了d-TeNT与3-马来酰亚胺丙酸n -羟基琥珀酰亚胺酯（BMPS）的活化反应，结果表明107个赖氨酸残基中有102个（95%）含有马来酰亚胺基团。其中只有22个Lys残基（20%）与RBD c端色氨酸（538CVNF541-HHHHHH）交联，可能是位阻作用所致。在LC-MS/MS分析之前，亲和层析对于确定缀合位点至关重要。携带共轭赖氨酸残基的线性肽和具有稳定连接形式（水解和环化）的2型肽，分别可以识别12个和18个偶联位点。RBD也与其他十种低丰度载体蛋白结合，但程度较轻。本研究首次报道了基于tt的结合疫苗的结合位点分配。

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引用次数: 0

Serum Proteome Profiling of Diabetic Patients Treated With DPP4 and SGLT2 Inhibitors Shows Improved Cognitive and Cardiovascular Functions 接受DPP4和SGLT2抑制剂治疗的糖尿病患者血清蛋白质组分析显示认知和心血管功能改善

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-17 DOI: 10.1002/pmic.70000

Md Abdul Hakim, Akeem Sanni, Shams T. Osman, Noha A. Hamdy, Waziha Tasnim Purba, Md Mostofa Al Amin Bhuiyan, Sherifdeen Onigbinde, Labiba K. El-Khordagui, Ahmed El-Yazbi, Yehia Mechref

Type 2 diabetes (T2D) is a complex metabolic disorder with rising global prevalence, leading to major complications such as cognitive decline, cardiovascular disease, and systemic inflammation. Although advances in T2D pharmacotherapy have shown promise in addressing these complications, the underlying protective mechanisms remain unclear, especially as they appear to be independent of glycemic control. In this study, we performed a comprehensive proteomic analysis using LC-MS/MS to explore the molecular effects of newer antidiabetic drugs, specifically dipeptidyl peptidase 4 (DPP4) and sodium-glucose cotransporter 2 (SGLT2) inhibitors (SGLT2is), when combined with metformin, the first-line treatment for T2D. Serum samples from 76 individuals were analyzed, including 16 healthy subjects, 32 T2D patients on metformin monotherapy, and 28 T2D patients receiving combination therapy. We identified and quantified 505 low-abundance proteins, followed by statistical analysis and ingenuity pathway analysis. Our findings revealed significant changes in key biological pathways related to synaptogenesis, insulin-like growth factor transport, and neurovascular coupling signaling. These results were further validated using parallel reaction monitoring. Notably, pathways associated with cognitive function and cardiovascular health were adversely affected in T2D patients on metformin monotherapy but showed improvement with combination therapy. These results suggest that the combination of DPP4 and SGLT2is offers a therapeutic advantage, underscoring the importance of personalized treatment strategies in managing T2D complications.

Summary: Type 2 diabetes (T2D) is a chronic metabolic disorder that contributes to the progression of cognitive impairment, cardiovascular diseases, and renal dysfunction. Cognitive decline in T2D patients can also increase the risk of developing neurological conditions like Alzheimer's disease.

Recently developed antidiabetic drugs have shown promising cardiovascular and renal health effects, such as dipeptidyl peptidase 4 (DPP4) inhibitors and sodium-glucose cotransporter 2 (SGLT2) inhibitors (SGLT2is). However, the precise mechanisms by which these drugs influence biological pathways related to cognitive function and central nervous system (CNS) development remain unclear.

In this study, we explored the impact of these newer antidiabetic drugs in combination with metformin, compared to metformin monotherapy and healthy controls, by investigating differentially expressed proteins and their role in cognitive processes.

Our findings reveal that DPP4 and SGLT2is activate key biological pathways—such as synaptogenesis, insulin-like growth factor regulation, and neurovascular coupling—that are either suppressed or not enriched in the metformin-only group. These pathways are critical for maintaining and regulating CNS function and cognitive h

2型糖尿病（T2D）是一种复杂的代谢紊乱，全球患病率不断上升，导致认知能力下降、心血管疾病和全身性炎症等主要并发症。尽管T2D药物治疗的进展已经显示出解决这些并发症的希望，但潜在的保护机制仍不清楚，特别是因为它们似乎与血糖控制无关。在这项研究中，我们使用LC-MS/MS进行了全面的蛋白质组学分析，以探索新型降糖药，特别是二肽基肽酶4 （DPP4）和钠-葡萄糖共转运蛋白2 （SGLT2）抑制剂（SGLT2is）与二甲双胍（T2D的一线治疗药物）联合使用时的分子效应。分析了76例患者的血清样本，包括16例健康受试者，32例单用二甲双胍治疗的T2D患者和28例联合治疗的T2D患者。我们对505个低丰度蛋白进行了鉴定和定量，然后进行了统计分析和独创性途径分析。我们的研究结果揭示了突触发生、胰岛素样生长因子运输和神经血管偶联信号相关的关键生物学通路的显著变化。通过平行反应监测进一步验证了这些结果。值得注意的是，与认知功能和心血管健康相关的途径在二甲双胍单药治疗的T2D患者中受到不利影响，但在联合治疗中表现出改善。这些结果表明，DPP4和SGLT2is联合治疗具有治疗优势，强调了个性化治疗策略在控制T2D并发症中的重要性。摘要：2型糖尿病（T2D）是一种慢性代谢性疾病，可导致认知障碍、心血管疾病和肾功能障碍的进展。T2D患者的认知能力下降也会增加患阿尔茨海默病等神经系统疾病的风险。最近开发的降糖药物已显示出良好的心血管和肾脏健康作用，如二肽基肽酶4 （DPP4）抑制剂和钠-葡萄糖共转运蛋白2 （SGLT2）抑制剂（SGLT2is）。然而，这些药物影响与认知功能和中枢神经系统（CNS）发育相关的生物学途径的确切机制尚不清楚。在这项研究中，我们通过研究差异表达蛋白及其在认知过程中的作用，探讨了这些新型降糖药与二甲双胍联合使用的影响，与单用二甲双胍和健康对照相比。我们的研究结果表明，DPP4和SGLT2is激活了关键的生物通路，如突触发生、胰岛素样生长因子调节和神经血管偶联，这些通路在单用二甲双胍组中要么被抑制，要么不被富集。这些通路对于维持和调节中枢神经系统功能和认知健康至关重要。

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引用次数: 0

Optimizing Proximity Proteomics on the EvoSep-timsTOF LC–MS System 基于EvoSep-timsTOF LC-MS系统的接近蛋白质组学优化

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-11 DOI: 10.1002/pmic.70010

Julia Kitaygorodsky, Brendon Seale, Vesal Kasmaeifar, Reuben Samson, Zhen-Yuan Lin, Martina Tersigni, Saya Sedighi, Cassandra J. Wong, Anne-Claude Gingras

<div> <section> <p>Proximity-dependent biotinylation (BioID) is a powerful means of exploring the cellular environments in which proteins reside. Expressing a protein of interest (bait) fused to a biotin ligase and adding biotin induces the covalent biotinylation of proximal partners (preys), which are recovered on streptavidin beads and identified by MS. However, a major technical limitation of BioID is peptide carryover into subsequent MS runs. This is typically mitigated via lengthy intersample wash cycles, which lowers throughput considerably. The aim of this study was to optimize BioID sample acquisition using an EvoSep LC system coupled to a timsTOF mass spectrometer, which has higher throughput and sensitivity than our current system, with less carryover. Our efforts resulted in an ∼15-fold increase in throughput using the 60 samples-per-day gradient with better sensitivity, and identifying nearly double the proteins found by our previously standardized workflow. Significance scoring also revealed more sensitive detection of high-confidence proximal interactions (∼1.5-fold) for five well-characterized baits, validating the new experimental workflow. Importantly, carryover was extremely limited, even without intersample washing, and limited to abundant proteins that are easily filtered during data analyses. Without washing, the newly optimized method can process 60 samples per day, using half of the sample amount previously required.</p> </section> <section> <h3> Summary</h3> <div> <ul> <li>Proximity-dependent biotinylation (PDB) coupled with MS is a powerful approach to characterize subcellular protein localization.</li> <li>However, the carry-over of peptides from the abundant proteins into subsequent MS runs is problematic. While this was previously mitigated by lengthy wash cycles of the chromatography column, this ultimately lowered throughput.</li> <li>The introduction of the EvoSep chromatography system and more sensitive MS instrumentation has enabled robust and fast analysis with lower sample amounts and minimal carry-over.</li> <li>To date, there has been no systematic evaluation of this EvoSep-timsTOF instrumentation for PDB, nor a direct comparison to a previously standardized workflow.</li> <li>This study compares the identifications between these acquisition setups, recommends sample loading and gradient settings for the EvoSep-timsTOF, and investigates the high-confidence proximal interactors identified.</li> <li>The results highlight the necessity of optimization of scoring approaches f

邻近依赖的生物素化（BioID）是探索蛋白质所在细胞环境的有力手段。将感兴趣的蛋白质（诱饵）融合到生物素连接酶中，并添加生物素，诱导近端伙伴（猎物）的共价生物素化，这些伙伴在链亲和素珠上被回收并通过质谱识别。然而，BioID的主要技术限制是肽携带到后续的质谱运行中。这通常通过长时间的样品清洗周期来缓解，这大大降低了吞吐量。本研究的目的是利用EvoSep LC系统与timsTOF质谱仪耦合来优化生物id样品采集，该系统比我们现有的系统具有更高的通量和灵敏度，并且结转更少。我们的努力使每天60个样品的通量增加了15倍，灵敏度更高，并且鉴定出的蛋白质几乎是我们以前标准化工作流程中发现的蛋白质的两倍。显著性评分还显示，对于五种特征良好的诱饵，高置信度近端相互作用的检测更敏感（~ 1.5倍），验证了新的实验工作流程。重要的是，即使没有样品间洗涤，携带也非常有限，并且仅限于在数据分析过程中容易过滤的丰富蛋白质。无需洗涤，新优化的方法每天可以处理60个样品，使用以前所需样品量的一半。摘要：邻近依赖的生物素化（PDB）与质谱结合是表征亚细胞蛋白定位的有力方法。然而，从丰富的蛋白质中携带多肽进入随后的MS运行是有问题的。虽然以前通过色谱柱的长洗涤周期可以减轻这种情况，但这最终降低了吞吐量。EvoSep色谱系统和更灵敏的质谱仪器的引入，使分析具有更低的样本量和最小的携带量。到目前为止，还没有对这种用于PDB的EvoSep-timsTOF仪器进行系统评估，也没有与以前标准化的工作流程进行直接比较。本研究比较了这些采集设置之间的鉴定，推荐了EvoSep-timsTOF的样品加载和梯度设置，并调查了鉴定的高置信度近端相互作用。结果强调了优化PDB评分方法的必要性，以及更快的MS方法，以最大限度地恢复已知的高置信度近端相互作用。重要的是，EvoSep- timstof系统大大提高了MS采集的有效吞吐量，因为可以消除样品之间的洗涤，而不会影响真正近端相互作用物的恢复，这可能是由于EvoSep色谱系统的结带减少和样品负载的减少。

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引用次数: 0

Issue Information: Proteomics 13ė25 发布信息：Proteomics 13ė25

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-10 DOI: 10.1002/pmic.70011

引用次数: 0

Memantine Administration Enhances Glutamatergic and GABAergic Pathways in the Human Hippocampus of Alzheimer's Disease Patients 美金刚处理增强阿尔茨海默病患者海马中的谷氨酸能和gaba能通路。

IF 3.9 4区生物学 Q2 BIOCHEMICAL RESEARCH METHODS

Proteomics

Pub Date : 2025-07-09 DOI: 10.1002/pmic.70006

Ivo Fabrik, Rudolf Kupcik, Daniela Fabrikova, Marketa Chvojkova, Kristina Holubova, Kristina Hakenova, Martin Horak, Jiri Soukup, Monika Manethova, Robert Rusina, Radoslav Matej, Ales Ryska, Ondrej Soukup

One of the traditional treatments in Alzheimer's disease (AD) is administration of memantine, the NMDA receptor antagonist. However, the molecular mechanism of the complex memantine action and the impact on the hippocampal proteome in humans is unknown. In this study, hippocampal proteins extracted from formalin-fixed paraffin-embedded post mortem tissues obtained from healthy donors (n = 15), AD patients not treated with memantine (n = 11), and AD patients treated with memantine (n = 8) were investigated using tandem mass tag (TMT)-based quantitative proteomics. Memantine medication induced subtle but distinct changes in the hippocampal proteome in AD patients. Although it did not prevent the metabolic and physiologic decline associated with AD pathology, memantine administration upregulated several mitochondrially encoded proteins and mitigated the proteomic pattern of activated phagocytes. Furthermore, memantine specifically enhanced the expression of postsynaptic glutamatergic and GABAergic receptors and components of the respective pathways without affecting presynaptic proteome. This suggests that memantine treatment in AD patients not only alleviates excitotoxic stress by inhibiting NMDA receptor activity, but also triggers broader adaptations in the synaptic signaling and plasticity.

阿尔茨海默病（AD）的传统治疗方法之一是使用NMDA受体拮抗剂美金刚。然而，复杂美金刚作用的分子机制及其对人类海马蛋白质组的影响尚不清楚。在这项研究中，从健康供体（n = 15）、未接受美金刚治疗的AD患者（n = 11）和接受美金刚治疗的AD患者（n = 8）的死后组织中提取的福尔马林固定石蜡提取的海马蛋白，采用基于tandem mass tag （TMT）的定量蛋白质组学方法进行研究。美金刚药物诱导AD患者海马蛋白组发生细微但明显的变化。虽然它不能阻止与AD病理相关的代谢和生理衰退，但美金刚给药上调了一些线粒体编码的蛋白质，并减轻了活化吞噬细胞的蛋白质组模式。此外，美金刚特异性地增强了突触后谷氨酸能和gaba能受体及其各自通路组分的表达，而不影响突触前蛋白质组。这表明，AD患者的美金刚治疗不仅可以通过抑制NMDA受体活性来缓解兴奋性毒性应激，还可以在突触信号传导和可塑性方面引发更广泛的适应。

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