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Investigation into Drug-Induced Liver Damage Using Multimodal Mass Spectrometry Imaging. 用多模态质谱成像研究药物性肝损害。
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2025-01-17 DOI: 10.1021/jasms.4c00313
Bryn Flinders, Lennart Huizing, Bhanu Singh, Heng-Keang Lim, Marjolein van Heerden, Filip Cuyckens, Ron M A Heeren, Rob J Vreeken

Drug toxicity during the development of candidate pharmaceuticals is the leading cause of discontinuation in preclinical drug discovery and development. Traditionally, the cause of the toxicity is often determined by histological examination, clinical pathology, and the detection of drugs and/or metabolites by liquid chromatography-mass spectrometry (LC-MS). While these techniques individually provide information on the pathological effects of the drug and the detection of metabolites, they cannot provide specific molecular spatial information without additional experiments. Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is a powerful, label-free technique for the simultaneous detection of pharmaceuticals, metabolites, and endogenous chemical species in tissue sections, which makes it suitable for mechanistic toxicological studies to directly correlate the distribution of the drug and its metabolites with histological findings. This capability was demonstrated by the analysis of the liver from dogs dosed with discontinued drug compound B and its N-desmethyl metabolite, compound A. Histological examination showed multifocal hepatocellular necrosis, bile duct hyperplasia, periportal fibrosis, and chronic inflammation. MALDI-MSI analysis of liver tissue dosed with only compound A indicated that liver lesions were associated exclusively with the parent compound, whereas liver lesions with compound B showed the presence of the parent compound and its two metabolites (compound A and an N-oxide metabolite). Using both positive and negative ion modes, simultaneous detection and identification of endogenous molecular markers of the connective tissue, blood vessels, liver parenchyma, and bile duct epithelium was achieved, allowing optimal visualization of histological lesions by mass spectrometry imaging.

候选药物开发过程中的药物毒性是临床前药物发现和开发中中断的主要原因。传统上,毒性的原因通常是通过组织学检查、临床病理和液相色谱-质谱(LC-MS)检测药物和/或代谢物来确定的。虽然这些技术单独提供有关药物的病理作用和代谢物检测的信息,但如果没有额外的实验,它们无法提供特定的分子空间信息。基质辅助激光解吸/电离-质谱成像(MALDI-MSI)是一种功能强大、无标记的技术,可同时检测组织切片中的药物、代谢物和内源性化学物质,这使得它适用于机械毒理学研究,直接将药物及其代谢物的分布与组织学结果联系起来。这种能力通过对服用停药化合物B及其n -去甲基代谢物化合物a的狗的肝脏进行分析得到证实。组织学检查显示多灶性肝细胞坏死、胆管增生、门静脉周围纤维化和慢性炎症。仅给药化合物A的肝脏组织MALDI-MSI分析表明,肝脏病变仅与母体化合物相关,而给药化合物B的肝脏病变显示母体化合物及其两种代谢物(化合物A和n -氧化物代谢物)的存在。使用正离子和负离子模式,可以同时检测和鉴定结缔组织、血管、肝实质和胆管上皮的内源性分子标记,从而通过质谱成像实现组织学病变的最佳可视化。
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引用次数: 0
Direct Implementation of MSn Using Frequency Scanning Collision Induced Dissociation in a Digital Ion Trap Mass Spectrometer. 在数字离子阱质谱仪中使用频率扫描碰撞诱导解离直接实现MSn。
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2024-12-23 DOI: 10.1021/jasms.4c00395
Jie Ren, Pingping Chen, Yunjing Zhang, Xingli He, Lingfeng Li, Peng Li

Tandem mass spectrometry (MSn) is one of the most effective methods to obtain the structures of organic molecules, enabling the observation of multigenerational ion fragments. Collision-induced dissociation (CID) is currently the most mature technique for mass spectrometry analysis. Ion trap mass spectrometry (ITMS) is favored for on-site detection field, due to its ability of MSn analysis with a single trap and its small size. However, conventional MSn analysis in ITMS requires repeated isolation and excitation processes multiple times, causing high complexity of the entire scanning process. Additionally, the fragment ion detection in ITMS is limited by low-mass cutoff (LMCO) and the weak fragmentation yield. In this study, a method named reverse scanning-collision induced dissociation (RS-CID) is proposed, which involves increasing RF and AC frequencies while maintaining RF voltage constant during the CID process. Twelve representative illegal drugs were analyzed adopting this method, enhancing the intensities of low-mass fragment ions compared to conventional dissociation method. Moreover, experimental results with ketamine and methamphetamine show that RS-CID effectively reduces the LMCO effect and slightly improves CID efficiency. It also enables direct acquisition of their multigeneration fragment ions spectra in a single sequence of ion injection, cooling, isolation, RS-CID, cooling, mass scanning and empty. The experiments to distinguish between the isomers ab-4en-pinaca and adb-3en-butinaca as well as the isomeric compounds 5f-cumyl-pegaclone and cumyl-pipetinaca were also successful by this method. In summary, RS-CID enables MSn analysis in a single sequence and improves the low-mass fragment ions intensity. It can simplify workflows, achieve faster analysis and provide more valuable mass spectral information.

串联质谱(MSn)是获得有机分子结构的最有效方法之一,可以观察多代离子片段。碰撞诱导解离(CID)是目前最成熟的质谱分析技术。离子阱质谱法(ITMS)因其单阱分析MSn的能力和体积小而受到现场检测领域的青睐。然而,传统的ITMS中MSn分析需要多次重复的分离和激励过程,导致整个扫描过程的复杂性很高。此外,ITMS中的碎片离子检测受到低质量截止(LMCO)和弱碎片产率的限制。本研究提出了一种反向扫描-碰撞诱导解离(RS-CID)方法,该方法在解离过程中增加射频和交流频率,同时保持射频电压恒定。采用该方法对12种具有代表性的非法药物进行了分析,与传统解离方法相比,该方法提高了低质量碎片离子的强度。此外,氯胺酮和甲基苯丙胺的实验结果表明,RS-CID可以有效地降低LMCO效应,并略微提高CID效率。它还可以在离子注入、冷却、分离、RS-CID、冷却、质量扫描和空化的单一序列中直接获取它们的多代碎片离子光谱。用该方法对异构体ab-4en-pinaca和ab- 3en-butinaca以及异构体5f-cumyl-pegaclone和cumyl-pipetinaca进行了成功的区分实验。总之,RS-CID可以在单个序列中进行MSn分析,并提高了低质量碎片离子强度。它可以简化工作流程,实现更快的分析并提供更有价值的质谱信息。
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引用次数: 0
NIST Mass Spectral Libraries in the Context of the Circular Economy of Plastics. 塑料循环经济背景下的NIST质谱库。
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2025-01-03 DOI: 10.1021/jasms.4c00349
Yamil Simón-Manso, Edward P Erisman, Tytus D Mak, Meghan C Burke, Adam Zuber, Xiaoyu Yang, Yuxue Liang, Pedatsur Neta, Tallat Bukhari, Antony J Williams, Joshua A Young, Samanthi Wickramasekara, William E Wallace, Stephen E Stein

The Mass Spectrometry Data Center (MSDC) has recently started improving existing libraries and creating new ones for identifying and analyzing plastics-related compounds (PRC) and materials (PRM) as part of the NIST circular economy program. PRC are small molecules of dissimilar chemical nature; hence, to increase coverage, we have used three types of ionizations: EI, ESI, and APCI. PRM are solids that include polymers, polymer mixtures, and commercial plastics, so we have used pyrolysis-gas chromatography (py-GC-MS) to create a new searchable library. First, we have increased the coverage of the existing libraries by including as many as possible commercially available PRC. Then, for testing the libraries and to deconvolute complex PRM mixtures, we have analyzed extractable and leachable (E&L) samples and pyrolysis products from one hundred standards of the most common polymers and some of their mixtures using LC-MS/MS, GC-MS, and py-GC-MS. In collaboration with the FDA, the EPA, and other non-government institutions, we are applying techniques, libraries, and tools to areas of interest to the circular economy of plastics, health risk assessments, and environmental challenges.

质谱数据中心(MSDC)最近开始改进现有的库,并创建新的库,用于识别和分析塑料相关化合物(PRC)和材料(PRM),这是NIST循环经济计划的一部分。PRC是化学性质不同的小分子;因此,为了增加覆盖率,我们使用了三种类型的电离:EI、ESI和APCI。PRM是固体,包括聚合物、聚合物混合物和商用塑料,因此我们使用热解-气相色谱法(py-GC-MS)创建了一个新的可搜索库。首先,我们增加了现有库的覆盖范围,包括尽可能多的商业可用PRC。然后,为了测试文库和反卷积复杂的PRM混合物,我们使用LC-MS/MS, GC-MS和py-GC-MS分析了100种标准的最常见聚合物及其混合物的可提取和可浸出(E&L)样品和热解产物。通过与FDA、EPA和其他非政府机构的合作,我们正在将技术、图书馆和工具应用于塑料循环经济、健康风险评估和环境挑战等相关领域。
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引用次数: 0
A Fast-Pass, Desorption Electrospray Ionization Mass Spectrometry Strategy for Untargeted Metabolic Phenotyping.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2025-01-27 DOI: 10.1021/jasms.4c00459
Hawkins S Shepard, Jody C May, Baltazar E Zuniga, Joshua P Abraham, Brian F Pfleger, Jamey D Young, John A McLean

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) provides direct analytical readouts of small molecules that can be used to characterize the metabolic phenotypes of genetically engineered bacteria. In an effort to accelerate the time frame associated with the screening of mutant libraries, we have developed a high-throughput DESI-MSI analytical workflow implementing a single raster line-scan strategy that facilitates the collection of location-resolved molecular information from engineered strains on a subminute time scale. Evaluation of this "Fast-Pass" DESI-MSI phenotyping workflow on analytical standards demonstrated the capability of acquiring full metabolic profiling information with a throughput of ∼40 s per sample. This Fast-Pass strategy was implemented in the analysis of genetically edited Escherichia coli strains that have been engineered to produce various free-fatty acids (FFAs) for applications relevant to biofuels. Due to the untargeted nature of DESI-MSI, the investigation of these strains yielded molecular information for both global metabolites and targeted detection of accumulated bioproducts, allowing simultaneous readouts of strain-specific chemical profiles and comparative measurements of FFA production levels.

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引用次数: 0
Reactivity of [CpFe(CO)2]+ with Nitrogen-Containing Heterocyclic Compounds in the Gas Phase: Ligand Exchange and Dehydrogenation.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2024-12-29 DOI: 10.1021/jasms.4c00437
Robert King, Allan J Canty, Richard A J O'Hair, Victor Ryzhov

A previous gas-phase study has uncovered formal catalytic cycles for the dehydrogenation of model liquid organic hydrogen carriers (LOHCs) pyrrolidine, N-methylpyrrolidine, and piperidine by the coordinatively unsaturated half-sandwich cyclopentadienyl iron cation, [CpFe]+. That work is extended here to the well-known condensed-phase [CpFe(CO)2]+ cation, which was generated via electrospray ionization for gas-phase reactions with model LOHCs in a linear ion trap mass spectrometer, in which the helium bath gas was seeded with 0.1% carbon monoxide. The initial ion-molecule reaction (IMR) was exothermic enough to expel one CO molecule from the complex to form [CpFe(CO)L]+ (L = pyrrolidine, N-methylpyrrolidine, or piperidine). Collision-induced dissociation (CID) of these cations revealed two fragmentation pathways: (i) removal of another CO molecule leading to the species [CpFeL]+ that was studied previously; (ii) dehydrogenation of the ligand L (except for L= N-methylpyrrolidine). Two new formal catalytic cycles (for dehydrogenation of pyrrolidine and piperidine) were found that operate via a combination of IMR and CID experiments and which rely on the presence of CO for re-ligation of iron complexes. Density functional theory calculations were performed to compute the structures of all species observed as well as the reaction energetics.

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引用次数: 0
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography-Mass Spectrometry Metabolomics Data Processing. Nextflow4MS-DIAL:可重复的液相色谱-质谱代谢组学数据处理Nextflow-Based工作流。
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2025-01-05 DOI: 10.1021/jasms.4c00364
Xinsong Du, Amanda Dobrowolski, Mathias Brochhausen, Timothy J Garrett, William R Hogan, Dominick J Lemas

Reproducibility in untargeted metabolomics data processing remains a significant challenge due to software limitations and the complex series of steps required. To address these issues, we developed Nextflow4MS-DIAL, a reproducible workflow for liquid chromatography-mass spectrometry (LC-MS) metabolomics data processing, validated with publicly available data from MetaboLights (MTBLS733). Nextflow4MS-DIAL automates LC-MS data processing to minimize human errors from manual data handling. The workflow supports software containerization, ensuring computational reproducibility and enabling collaborative research. Nextflow4MS-DIAL is compatible with any Unix-like system and supports multiple job schedulers, offering flexibility and ease of use. The Nextflow4MS-DIAL workflow is available under the permissive MIT license: https://github.com/Nextflow4Metabolomics/nextflow4ms-dial.

由于软件限制和所需的一系列复杂步骤,非靶向代谢组学数据处理的可重复性仍然是一个重大挑战。为了解决这些问题,我们开发了Nextflow4MS-DIAL,这是一种可重复的液相色谱-质谱(LC-MS)代谢组学数据处理工作流程,通过MetaboLights (MTBLS733)的公开数据进行验证。Nextflow4MS-DIAL自动LC-MS数据处理,以尽量减少人工数据处理的人为错误。该工作流支持软件容器化,确保计算的可重复性并使协作研究成为可能。Nextflow4MS-DIAL与任何类unix系统兼容,并支持多个作业调度器,提供灵活性和易用性。Nextflow4MS-DIAL工作流可在MIT许可下获得:https://github.com/Nextflow4Metabolomics/nextflow4ms-dial。
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引用次数: 0
Unified Fragmentation Pathways of Lithiated, Longer-Chain Acylglycerols Can Be Identified from Tandem Mass Spectrometry and Density Functional Computations. 统一的碎片化途径,长链酰基甘油可以识别从串联质谱和密度泛函计算。
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2025-01-20 DOI: 10.1021/jasms.4c00423
J Stuart Grossert, Louis Ramaley

We extend our previous work on the energetics and mechanisms of fragmentation in the mass spectrometry of triacylglycerols (TAGs). Previously, we proposed viable mechanisms for the collision-induced fragmentation of lithiated tripropionylglycerol using triple-quadrupole mass spectrometry. In this work, we used a QqLIT mass spectrometer to study both double- and triple-stage spectra from a range of TAGs having acid chains of types AAA (identical acid chains), AAB, ABA, and ABC, with chain lengths of 6-18 carbon atoms; we also studied some TAGs having a single double bond in the Δ-9 position. Detailed computations on fragmentation pathways were carried out on lithiated trihexanoylglycerol and on a limited number of longer chain ions. Second-stage fragmentations led to the formation of a lithiated ion after the loss of a neutral acid. With a further input of energy, this ion could rearrange into two other ions, one being formed more easily than the other. In a triple-stage fragmentation, these three ions give a defined series of product ions, some of which are characteristic of the substitution pattern on the glycerol core of the TAG. Computed reaction energies for product ion formation showed comparable trends to the relative intensities of the observed product ion spectra. These results have enabled us to propose unified mechanisms for the double- and triple-stage fragmentation of lithiated TAGs. The mechanisms have reasonable energetics, and all ions, as well as saddle points, have viable geometries. In addition, the fragmentation mechanisms are in accord with all the published experimental mass spectra.

我们扩展了之前在质谱分析中对三酰基甘油(TAGs)断裂的能量学和机制的研究。在此之前,我们使用三重四极杆质谱法提出了碰撞诱导的锂化三丙酰甘油碎片化的可行机制。在这项工作中,我们使用QqLIT质谱仪研究了一系列具有AAA(相同酸链),AAB, ABA和ABC类型的酸链,链长为6-18个碳原子的标签的二级和三级光谱;我们还研究了一些在Δ-9位置上有一个单双键的标签。对锂化三己醇甘油和有限数量的长链离子的断裂路径进行了详细的计算。第二阶段的碎裂导致在失去中性酸后形成锂离子。随着能量的进一步输入,这个离子可以重新排列成另外两个离子,其中一个比另一个更容易形成。在三段裂解中,这三种离子产生一系列确定的产物离子,其中一些在TAG的甘油核上具有取代模式的特征。计算出的生成离子的反应能与观察到的生成离子光谱的相对强度有相似的趋势。这些结果使我们能够提出锂化标签的双阶段和三阶段碎片化的统一机制。该机制具有合理的能量学,并且所有离子以及鞍点都具有可行的几何形状。此外,破碎机制与所有已发表的实验质谱一致。
{"title":"Unified Fragmentation Pathways of Lithiated, Longer-Chain Acylglycerols Can Be Identified from Tandem Mass Spectrometry and Density Functional Computations.","authors":"J Stuart Grossert, Louis Ramaley","doi":"10.1021/jasms.4c00423","DOIUrl":"10.1021/jasms.4c00423","url":null,"abstract":"<p><p>We extend our previous work on the energetics and mechanisms of fragmentation in the mass spectrometry of triacylglycerols (TAGs). Previously, we proposed viable mechanisms for the collision-induced fragmentation of lithiated tripropionylglycerol using triple-quadrupole mass spectrometry. In this work, we used a QqLIT mass spectrometer to study both double- and triple-stage spectra from a range of TAGs having acid chains of types AAA (identical acid chains), AAB, ABA, and ABC, with chain lengths of 6-18 carbon atoms; we also studied some TAGs having a single double bond in the Δ-9 position. Detailed computations on fragmentation pathways were carried out on lithiated trihexanoylglycerol and on a limited number of longer chain ions. Second-stage fragmentations led to the formation of a lithiated ion after the loss of a neutral acid. With a further input of energy, this ion could rearrange into two other ions, one being formed more easily than the other. In a triple-stage fragmentation, these three ions give a defined series of product ions, some of which are characteristic of the substitution pattern on the glycerol core of the TAG. Computed reaction energies for product ion formation showed comparable trends to the relative intensities of the observed product ion spectra. These results have enabled us to propose unified mechanisms for the double- and triple-stage fragmentation of lithiated TAGs. The mechanisms have reasonable energetics, and all ions, as well as saddle points, have viable geometries. In addition, the fragmentation mechanisms are in accord with all the published experimental mass spectra.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"368-378"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142998196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis and Characterization of Poly(ethylene furanoate)/Poly(ε-caprolactone) Block Copolymers. 聚呋喃酸乙烯/聚ε-己内酯嵌段共聚物的合成与表征
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2025-01-09 DOI: 10.1021/jasms.4c00397
Johan Stanley, Lidia Molina-Millán, Chrys Wesdemiotis, Ron M A Heeren, Alexandra Zamboulis, Lidija Fras Zemljič, Dimitra A Lambropoulou, Dimitrios N Bikiaris

Biobased poly(ethylene furanoate) (PEF)/poly(ε-caprolactone) (PCL) block copolymers have been synthesized using ring opening polymerization (ROP) of ε-caprolactone (ε-CL) in the presence of PEF in different mass ratios. An increase in intrinsic viscosity is observed for the block copolymers with higher ε-CL content due to the extension of their macromolecular chain. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MS) was employed to understand the composition and structure of the produced block copolymers. The MS analysis helped to confirm the formation of PEF-PCL copolymers in all cases. Furthermore, tandem mass spectrometry experiments were performed to analyze the intrinsic fragmentation mechanism of neat PEF and PCL (both linear and cyclic) and confirm the block structure and end-groups. Finally, nuclear magnetic resonance results confirmed the composition and microstructure of the block copolymers. The synthesized PEF-PCL block copolymers can be used as a replacement for petroleum derived plastics, especially in the field of food packaging.

以ε-己内酯(ε-CL)为原料,在不同质量比的聚戊酸乙烯(PEF)存在下,采用开环聚合(ROP)法制备了生物基聚呋喃酸乙烯(PEF)/聚ε-己内酯(PCL)嵌段共聚物。ε-CL含量较高的嵌段共聚物,由于其大分子链的延伸,其特性粘度增加。采用基质辅助激光解吸电离飞行时间质谱(MS)分析了所制嵌段共聚物的组成和结构。质谱分析有助于确认所有情况下PEF-PCL共聚物的形成。此外,通过串联质谱实验分析了纯PEF和PCL(线性和循环)的内在断裂机理,并确定了块体结构和端基。最后,核磁共振结果证实了嵌段共聚物的组成和微观结构。合成的PEF-PCL嵌段共聚物可作为石油衍生塑料的替代品,特别是在食品包装领域。
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引用次数: 0
Locating Polyubiquitin Receptors on the 19S Regulatory Proteasome of S. cerevisiae by Cross-Linking Mass Spectrometry.
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2025-01-22 DOI: 10.1021/jasms.4c00381
Yiran Ma, Bingqing Zhao, Amit K S Gautam, Caroline Davis, Jonathan C Trinidad, James P Reilly, David E Clemmer, Andreas Matouschek

The effectiveness of state-of-the-art cross-linking strategies and mass spectrometry (MS) detection was explored in an important biological context, namely, the ubiquitin-proteasome system, which is responsible for most of the regulated protein degradation in eukaryotic cells. The locations of possible binding sites on the S. cerevisiae 19S proteasome regulatory particle for Lys48 linked polyubiquitin chains were examined using cross-linking strategies and MS based detection by comparing two types of cross-linkers: a (bis)-sulfosuccinimidyl suberate (BS3) and diethyl suberothioimidate (DEST). The well-established BS3-based strategy produced 328 cross-linked peptides; however, no ubiquitin-19S cross-links were observed. The recently developed DEST-based approach produced fewer (146) linkages overall, but these included six ubiquitin-19S cross-links. Some of these cross-links are predicted by the canonical view of ubiquitin recognition, but others suggest novel insights into how the proteasome recognizes its substrates. A discussion of these strategies and structural implications for polyubiquitin-proteasome binding is provided.

{"title":"Locating Polyubiquitin Receptors on the 19S Regulatory Proteasome of <i>S. cerevisiae</i> by Cross-Linking Mass Spectrometry.","authors":"Yiran Ma, Bingqing Zhao, Amit K S Gautam, Caroline Davis, Jonathan C Trinidad, James P Reilly, David E Clemmer, Andreas Matouschek","doi":"10.1021/jasms.4c00381","DOIUrl":"10.1021/jasms.4c00381","url":null,"abstract":"<p><p>The effectiveness of state-of-the-art cross-linking strategies and mass spectrometry (MS) detection was explored in an important biological context, namely, the ubiquitin-proteasome system, which is responsible for most of the regulated protein degradation in eukaryotic cells. The locations of possible binding sites on the <i>S. cerevisiae</i> 19S proteasome regulatory particle for Lys<sup>48</sup> linked polyubiquitin chains were examined using cross-linking strategies and MS based detection by comparing two types of cross-linkers: a (bis)-sulfosuccinimidyl suberate (BS<sup>3</sup>) and diethyl suberothioimidate (DEST). The well-established BS<sup>3</sup>-based strategy produced 328 cross-linked peptides; however, no ubiquitin-19S cross-links were observed. The recently developed DEST-based approach produced fewer (146) linkages overall, but these included six ubiquitin-19S cross-links. Some of these cross-links are predicted by the canonical view of ubiquitin recognition, but others suggest novel insights into how the proteasome recognizes its substrates. A discussion of these strategies and structural implications for polyubiquitin-proteasome binding is provided.</p>","PeriodicalId":672,"journal":{"name":"Journal of the American Society for Mass Spectrometry","volume":" ","pages":"277-285"},"PeriodicalIF":3.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gas-Phase Unfolding Reveals Stability Shifts Associated with Substrate Binding in Modular Polyketide Synthases. 气相展开揭示模块化多酮合成酶中与底物结合相关的稳定性转变
IF 3.1 2区 化学 Q2 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-02-05 Epub Date: 2024-07-25 DOI: 10.1021/jasms.4c00179
Chunyi Zhao, Nicholas B Borotto, Jennifer Schmidt, Kinshuk Srivastava, Andrew Lowell, Kristina Hakansson, David H Sherman, Brandon T Ruotolo

Native mass spectrometry (MS), ion mobility (IM), and collision-induced unfolding (CIU) have all been widely used to study the binding of small molecules to proteins and their complexes. Despite many successes in detecting subtle gas-phase stability differences in smaller systems dominated by single-domain subunits, studies targeting complexes comprised of large, multidomain subunits still face many challenges. For example, polyketide synthases (PKSs) are multiprotein enzymes that use their modular architecture to produce polyketide natural products and form the basis for nearly one-third of pharmaceuticals. Here, we describe the development of CIU methods capable of extracting information from these multiprotein complexes and demonstrate the current limits of quantitative CIU technology by probing the stabilities ∼280 kDa PKS dimer protein complexes. Our approach detects the evidence of the stability shifts associated with substrate binding that accounts for <0.1% of the mass for the intact assembly.

原位质谱(MS)、离子迁移率(IM)和碰撞诱导展开(CIU)都被广泛用于研究小分子与蛋白质及其复合物的结合。尽管在检测以单链亚基为主的较小系统中微妙的气相稳定性差异方面取得了许多成功,但针对由大型多链亚基组成的复合物的研究仍然面临许多挑战。例如,多酮合成酶(PKSs)是一种多蛋白酶,利用其模块化结构生产多酮天然产物,是近三分之一药物的基础。在这里,我们介绍了能够从这些多蛋白复合物中提取信息的 CIU 方法的发展情况,并通过探测 PKS 二聚体蛋白复合物 ∼280 kDa 的稳定性,证明了目前定量 CIU 技术的局限性。我们的方法可以检测到与底物结合相关的稳定性变化的证据,而底物结合的原因包括
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引用次数: 0
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Journal of the American Society for Mass Spectrometry
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