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Evaluation of Recent Data Processing Strategies on Q-TOF LC/MS Based Untargeted Metabolomics 基于Q-TOF LC/MS的非靶向代谢组学最新数据处理策略评价
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.1.1
O. Kaplan, M. Çelebier
In this study, some of the recently reported data processing strategies were evaluated and modified based on their capabilities and a brief workflow for data mining was redefined for Q-TOF LC-MS based untargeted metabolomics. Commercial pooled human plasma samples were used for this purpose. An ultrafiltration procedure was applied on sample preparation. Sample set was analyzed through Q-TOF LC/MS. A C18 column (Agilent Zorbax 1.8 μM, 50 × 2.1 mm) was used for chromatographic separation. Raw chromatograms were processed using XCMS - R programming language edition and Isotopologue Parameter Optimization (IPO) was used to optimize XCMS parameters. The raw XCMS table was processed using MS Excel to find reliable and reproducible peaks. Totally 1650 reliable and reproducible potential metabolite peaks were found based on the data processing procedures given in this paper. The redefined dataset was upload into MetaboAnalyst platform and the identified metabolites were matched with 86 metabolic pathways. Thus, two list were obtained and presented in this study as supplement files. The first list is to present the retention times and m/z values of detected metabolite peaks. The second list is the metabolic pathways related with the identified metabolites. The briefly described data processing strategies and dataset presented in this study could be beneficial for the researchers working on untargeted metabolomics for processing their data and validating their results.
在这项研究中,一些最近报道的数据处理策略根据其能力进行了评估和修改,并为基于Q-TOF LC-MS的非靶向代谢组学重新定义了数据挖掘的简要工作流程。商业汇集的人类血浆样本用于此目的。采用超滤法制备样品。采用Q-TOF LC/MS对样品集进行分析。色谱柱为C18 (Agilent Zorbax 1.8 μM, 50 × 2.1 mm)。采用XCMS - R编程语言对原始色谱进行处理,并采用同位素参数优化(IPO)对XCMS参数进行优化。使用MS Excel对原始XCMS表进行处理,寻找可靠且可重现的峰。根据本文给出的数据处理程序,共发现了1650个可靠且可重复的潜在代谢物峰。重新定义的数据集被上传到MetaboAnalyst平台,鉴定出的代谢物与86种代谢途径相匹配。因此,获得了两个列表,并在本研究中作为补充文件提出。第一个列表是检测到的代谢物峰的保留时间和m/z值。第二张表是与已鉴定的代谢物相关的代谢途径。本研究中简要描述的数据处理策略和数据集可能有助于研究非靶向代谢组学的研究人员处理其数据并验证其结果。
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引用次数: 4
Simultaneous Determination of Anthraquinone, Flavonoids, and Phenolic Antidiabetic Compounds from Cassia auriculata Seeds by Validated UHPLC Based MS/MS Method 高效液相色谱-质谱法同时测定木耳决明子中蒽醌类、黄酮类和酚类抗糖尿病化合物的含量
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.4.82
A. Girme, G. Saste, Ashish A. Chinchansure, S. Joshi, R. Kunkulol, L. Hingorani, B. Patwardhan
A systematic isolation and characterization study for Cassia auriculata (CA) seeds resulted in identifying antidiabetic compounds 1,3,8-trihydroxyanthraquinone and quercetin, quercetin-3-O-rutinoside, gallic acid, caffeic acid, ferulic acid, and ellagic acid. The ultra-high-performance liquid chromatography based triple quadrupole mass spectrometry methodology was developed and validated for simultaneous identification and confirmation of these compounds from CA seeds. Multiple reaction monitoring (MRM) based quantification method was developed with MRM optimizer software for MS1 and MS2 mass analysis. The method was optimized on precursor ions and product ions with the ion ratio of each compound. The calibration curves of seven bioactive analytes showed excellent linearity (r2 ≥ 0.99). The quantitation results found precise (RSD, < 10 %) with good recoveries (84.58 to 101.42%). The matrix effect and extraction recoveries were found within the range (91.66 to 102.11%) for the CA seeds. This is the first MS/MS-based methodology applied to quantifying seven antidiabetic compounds in CA seeds and its extract for quality control purposes.
对auriculata (CA)种子进行了系统的分离和鉴定,鉴定出抗糖尿病化合物1,3,8-三羟基蒽醌和槲皮素、槲皮素-3- o - rutino苷、没食子酸、咖啡酸、阿魏酸和鞣花酸。建立了以超高效液相色谱为基础的三重四极杆质谱分析方法,并对该方法进行了验证。采用多反应监测(MRM)优化软件,建立了基于多反应监测的MS1和MS2质谱定量分析方法。该方法对前驱体离子和产物离子进行了优化,并对每种化合物的离子比进行了优化。7种生物活性分析物的校准曲线线性良好(r2≥0.99)。定量结果精确(RSD < 10%),加样回收率为84.58 ~ 101.42%。提取回收率在91.66 ~ 102.11%范围内。这是首次应用质谱/质谱方法定量测定草籽及其提取物中7种抗糖尿病化合物的质量控制目的。
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引用次数: 1
Analysis of Hypoxia-Inducible Factor Stabilizers by a Modified QuEChERS Extraction for Antidoping Analysis 用改良的QuEChERS萃取法分析缺氧诱导因子稳定剂的反兴奋剂分析
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.4.118
S. Kim, Nu Ri Lim, H. Min, Changmin Sung, H. Oh, Ki Hun Kim
An analytical method was developed for hypoxia-inducible factor (HIF) stabilizers based on QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) sample preparation and liquid chromatography-high resolution mass spectrometry analysis. HIF stabilizers potentially enhance the performance of athletes, and hence, they have been prohibited. However, the analysis of urinary HIF stabilizers is not easy owing to their unique structure and characteristics. Hence, we developed the QuEChERS preparation technique for a complementary method and optimized the pH, volume of extraction solvent, and number of extractions. We found that double extraction with 1% of formic acid in acetonitrile provided the highest recovery of HIF stabilizers. Moreover, the composition of the mobile phase was also optimized for better separation of molidustat and IOX4. The developed method was validated in terms of its precision, detection limit, matrix effect, and recovery for ISO accreditation. To the best of our knowledge, this is the first demonstration of the application of the QuEChERS method, which is suitable as a complementary analytical method, in antidoping.
建立了一种基于QuEChERS(快速、简便、廉价、有效、坚固、安全)样品制备和液相色谱-高分辨质谱分析的低氧诱导因子(HIF)稳定剂分析方法。HIF稳定剂可能会提高运动员的表现,因此,它们被禁止使用。然而,由于其独特的结构和特性,分析尿HIF稳定剂并不容易。因此,我们开发了QuEChERS制备技术作为补充方法,并优化了提取溶剂的pH、体积和提取次数。结果表明,在乙腈中以1%甲酸进行二次萃取时,HIF稳定剂的回收率最高。此外,还对流动相的组成进行了优化,以更好地分离莫里司他和IOX4。对该方法的精密度、检出限、基质效应和回收率进行了验证。据我们所知,这是QuEChERS方法的第一次应用演示,它适合作为一种补充分析方法,用于反兴奋剂。
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引用次数: 2
A Low-Cost Open-Source Air Sampler for the Sorbent Tube Sampling for TD-GC/MS Analysis 一种低成本的开源空气采样器,用于吸附管采样的TD-GC/MS分析
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.4.95
Hwa-yong Jang, H. Oh
In this study, we provide full descriptions of how to make a low-cost and completely open-source laboratory-made air sampler that will be used for sample adsorption for thermal desorption-gas chromatography mass spectrometry (TD-GC/MS) analysis. It is well known that harmful gases cause bad effects on human bodies, so it is necessary to identify the types and amounts of gases in industrial sites. One of the most commonly used methods for gas sampling is to utilize a sorbent tube using an air sampler. Commercially available air samplers are expensive, typically priced between $1,000 and $2,000, and their design often cannot be modified to fit the experiment. To address these shortcomings, we have developed a do-it-yourself (DIY) air sampler that is not only cheap enough, but also completely open-source. Furthermore, the performance of the fabricated air sampler was validated in conjunction with TD-GC/MS for the analysis of volatile compounds.
在这项研究中,我们提供了如何制作一个低成本和完全开源的实验室自制空气采样器的完整描述,该采样器将用于样品吸附进行热解吸-气相色谱-质谱(TD-GC/MS)分析。众所周知,有害气体对人体有不良影响,因此有必要确定工业场所气体的种类和数量。气体取样最常用的方法之一是使用空气取样器的吸收管。市售的空气采样器价格昂贵,通常在1000美元到2000美元之间,而且它们的设计往往不能修改以适应实验。为了解决这些缺点,我们开发了一种自己动手(DIY)的空气采样器,它不仅足够便宜,而且完全开源。此外,结合TD-GC/MS分析挥发性化合物,验证了制作的空气采样器的性能。
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引用次数: 0
Comparison of Matrices for Optimal Analysis of Synthetic Polymers Using MALDI-TOF Mass Spectrometry MALDI-TOF质谱法分析合成聚合物最佳基质的比较
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.4.77
HeeJae Yoo, Duck-Hyun Kim, Yoon-Ji Choi, Jungshin Choi, Moonhee Park, DongJin Shin, YoonSeok Oh, Yangsun Kim, Kun Cho
Characterization of the various chemical aspects of composite polymers is important for quality control of manufactured polymers. In this study, we compared three suitable matrices (α cyano-4-hydroxycinnamic acid [CHCA], 2,5 dihydroxy benzoic acid [2,5-DHB], and dithranol), to characterize various synthetic polymers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Although the spectra obtained with the CHCA and 2,5-DHB matrices were generally good, in certain samples ghost peaks disappeared only when dithranol was used as the matrix. Furthermore, we examined the use of sodium trifluoroacetate (NaTFA) as an additive to reduce interference by metals and copolymers in the spectra. In conclusion, appropriate selection of a matrix, according to the characteristics of the polymer, and the use of additives to improve sensitivity are important considerations for polymer analysis and development.
表征复合聚合物的各种化学方面对制造聚合物的质量控制是重要的。在这项研究中,我们比较了三种合适的基质(α氰基-4-羟基肉桂酸[CHCA], 2,5二羟基苯甲酸[2,5- dhb]和二糖醇),用基质辅助激光解吸/电离飞行时间质谱法来表征各种合成聚合物。虽然用CHCA和2,5- dhb基质得到的光谱一般都很好,但在某些样品中,只有当用双乙醇作为基质时才会出现鬼峰。此外,我们研究了使用三氟乙酸钠(NaTFA)作为添加剂来减少光谱中金属和共聚物的干扰。综上所述,根据聚合物的特性选择合适的基质,并使用添加剂来提高灵敏度是聚合物分析和发展的重要考虑因素。
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引用次数: 0
Advances in Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS)-Based Techniques for Elucidating Higher-Order Protein Structures 基于离子迁移谱-质谱(IMS-MS)技术的高阶蛋白质结构研究进展
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.4.65
Jongcheol Seo
Despite its great success in the field of proteomics, mass spectrometry has limited use for determining structural details of peptides, proteins, and their assemblies. Emerging ion mobility spectrometry-mass spectrometry has enabled us to explore the conformational space of protein ions in the gas phase, and further combinations with the gas-phase ion spectroscopy and the collision-induced unfolding have extended its abilities to elucidating the secondary structure and local details of conformational transitions. This review will provide a brief introduction to the combined approaches of IMS-MS with gas-phase ion infrared spectroscopy or collision-induced unfolding and their most recent results that successfully revealed higher-order structural details.
尽管质谱法在蛋白质组学领域取得了巨大的成功,但它在确定肽、蛋白质及其组装的结构细节方面的应用有限。新兴的离子迁移谱-质谱使我们能够探索蛋白质离子在气相中的构象空间,并且进一步结合气相离子光谱和碰撞诱导展开扩展了其阐明二级结构和构象转变的局部细节的能力。本文将简要介绍IMS-MS与气相离子红外光谱或碰撞诱导展开相结合的方法,以及它们最近成功揭示高阶结构细节的结果。
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引用次数: 0
Mass Spectrometry-Based Proteomic Profiling of Pseudopodia of Metastatic Cancer Cells 基于质谱的转移癌细胞假足的蛋白质组学分析
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.2.25
Sunkyu Choi
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引用次数: 1
Mass Spectrometry Imaging of Microbes 微生物质谱成像
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.3.41
Hyojik Yang, D. Goodlett, R. Ernst, Alison J. Scott
Microbes influence many aspects of human life from the environment to health, yet evaluating their biological processes at the chemical level can be problematic. Mass spectrometry imaging (MSI) enables direct evaluation of microbial chemical processes at the atomic to molecular levels without destruction of valuable two-dimensional information. MSI is a label-free method that allows multiplex spatiotemporal visualization of atomic- or molecular-level information of microbial and microberelated samples. As a result, microbial MSI has become an important field for both mass spectrometrists and microbiologists. In this review, basic techniques for microbial MSI, such as ionization methods and analyzers, are explored. In addition, we discuss practical applications of microbial MSI and various data-processing techniques.
微生物影响人类生活的许多方面,从环境到健康,但在化学水平上评估它们的生物过程可能是有问题的。质谱成像(MSI)可以在原子到分子水平上直接评估微生物化学过程,而不会破坏有价值的二维信息。MSI是一种无标签的方法,允许对微生物和微生物相关样品的原子或分子水平信息进行多重时空可视化。因此,微生物MSI已成为质谱和微生物学家的一个重要领域。在这篇综述中,探讨了微生物MSI的基本技术,如电离方法和分析仪。此外,我们还讨论了微生物微si和各种数据处理技术的实际应用。
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引用次数: 3
Liquid Chromatography-Tandem Mass Spectrometry Analysis of Riboflavin in Beagle Dog Plasma for Pharmacokinetic Studies 液相色谱-串联质谱法分析比格犬血浆中核黄素的药动学研究
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.1.10
Hyeon Myeong Jeong, B. Shin, Soyoung Shin
Riboflavin is a water-soluble vitamin, which serves as a precursor to flavin mononucleotide and flavin adenine dinucleotide. This study aimed to develop a simple and rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis for the quantification of riboflavin in the Beagle dog plasma. This method utilized simple protein precipitation with acetonitrile and 13C4,15N2-riboflavin was used as an internal standard (IS). For chromatographic separation, a hydrophilic interaction liquid chromatography (HILIC) column was used with gradient elution. The mobile phase consisted of 0.1% (v/v) aqueous formic acid with 10 mM ammonium formate and acetonitrile with 0.1% (v/v) formic acid. Since riboflavin is an endogenous compound, 4% bovine serum albumin in phosphate buffered saline was used as a surrogate matrix to prepare the calibration curve. The quantification limit for riboflavin in the Beagle dog plasma was 5 ng/mL. The method was fully validated for its specificity, sensitivity, accuracy and precision, recovery, and stability according to the US FDA guidance. The developed LC-MS/MS method may be useful for the in vivo pharmacokinetic studies of riboflavin.
核黄素是一种水溶性维生素,是黄素单核苷酸和黄素腺嘌呤二核苷酸的前体。本研究旨在建立一种简便、快速的液相色谱-串联质谱(LC-MS/MS)分析方法,定量测定比格犬血浆中核黄素的含量。该方法采用乙腈简单蛋白沉淀法,以13C4, 15n2 -核黄素为内标。色谱分离采用亲水性相互作用液相色谱(HILIC)柱,梯度洗脱。流动相为0.1% (v/v)甲酸水溶液- 10 mM甲酸铵和0.1% (v/v)甲酸乙腈。由于核黄素是一种内源性化合物,因此以磷酸缓冲盐水中4%牛血清白蛋白作为替代基质制备校准曲线。比格犬血浆中核黄素的定量限为5 ng/mL。该方法的特异性、敏感性、准确度和精密度、回收率和稳定性根据美国FDA指南进行了充分验证。建立的LC-MS/MS方法可用于核黄素体内药代动力学研究。
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引用次数: 2
Mass Spectrometry for Metabolome Analysis 代谢组分析的质谱分析
IF 0.5 Q4 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-01-01 DOI: 10.5478/MSL.2020.11.2.17
Xiaohang Wang, Liang Li
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引用次数: 0
期刊
Mass Spectrometry Letters
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