Article
Chemistry, Analytical
Teresa S. McMillen, Andrew Leslie, Kenneth Chisholm, Susanne Penny, Jeffrey Gallant, Alejandro Cohen, Arik Drucker, James P. Fawcett, Devanand M. Pinto
Summary: This study presents a comprehensive and quantitatively robust method for metabolomic analysis, using HILIC and RP stationary phases combined with positive and negative electrospray ionization. The method allows for complete analysis of a single sample in as little as 40 minutes and has been validated with clinical samples.
ANALYTICA CHIMICA ACTA
(2023)
Article
Multidisciplinary Sciences
Taiyun Kim, Owen Tang, Stephen T. Vernon, Katharine A. Kott, Yen Chin Koay, John Park, David E. James, Stuart M. Grieve, Terence P. Speed, Pengyi Yang, Gemma A. Figtree, John F. O'Sullivan, Jean Yee Hwa Yang
Summary: A new computational workflow is developed to remove unwanted data variation while preserving biologically relevant information in large scale metabolomics studies.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Ken H. Liu, Choon M. Lee, Grant Singer, Preeti Bais, Francisco Castellanos, Michael H. Woodworth, Thomas R. Ziegler, Colleen S. Kraft, Gary W. Miller, Shuzhao Li, Young-Mi Go, Edward T. Morgan, Dean P. Jones
Summary: The study introduces a novel method in which xenobiotic metabolites are enzymatically generated and identified using high-resolution mass spectrometry, offering a new approach for exposomics research.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Zhuoru He, Zhongqiu Liu, Lingzhi Gong
Summary: The all-in-one sample preparation method MeOH-MTBE-H2O (1:5:1.5, v/v/v) was identified as the optimal extraction method for plasma metabolomics. In the study of osteoarthritis (OA), a panel of biomarkers including cholesterol, lactic acid, stearic acid, alpha-tocopherol, and oxalic acid showed potential as diagnostic biomarkers for distinguishing OA patients from healthy controls.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Pharmacology & Pharmacy
Qing-Qing Yu, Heng Zhang, Shiyuan Zhao, Dadi Xie, Haibo Zhao, Weidong Chen, Min Pang, Baoqin Han, Pei Jiang
Summary: This study comprehensively analyzed the metabolite changes in a mouse model of irinotecan-induced intestinal mucositis, identifying 46 metabolites with significant changes in tissues and serum. The study highlighted key pathways related to these metabolites, offering insights into new biomarkers for diagnosis and treatment of intestinal mucositis.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Endocrinology & Metabolism
Jun Kou, Chunyang He, Lin Cui, Zhengping Zhang, Wei Wang, Li Tan, Da Liu, Wei Zheng, Wei Gu, Ning Xia
Summary: The study on Chinese postmenopausal women with osteoporosis identified potential biomarkers related to metabolic pathway disorders, providing new insights for early diagnosis. The findings suggest that metabonomic analysis has great potential for application in postmenopausal women with osteoporosis.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Chemistry, Analytical
Eliska Ivanovova, Barbora Pisklakova, Dana Dobesova, Ales Kvasnicka, David Friedecky
Summary: Diagnosing a large group of inborn errors of metabolism poses a challenge for physicians due to non-specific clinical symptoms, leading to the importance of laboratory methods for differential diagnosis. Liquid chromatography and mass spectrometry (LC-MS) technology has significantly expanded diagnostic possibilities in the last two decades. It has been used for multicomponent analysis of metabolites, as well as successfully applied in metabolomics and lipidomics to discover new potential biomarkers.
MICROCHEMICAL JOURNAL
(2021)
Article
Medical Laboratory Technology
Yuyang Hou, Yuanping He, Jingjie Wang, Yanfen Zhou, Bo Ma, Xin Li, Liang Shi, Qi Zhang
Summary: By analyzing the metabolic profiles of four different types of asthenozoospermia, this study revealed abnormal changes in metabolites and metabolic pathways associated with the disease. The findings provide new clues and evidence for the etiology, diagnosis, and treatment of asthenozoospermia.
CLINICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Frantisek Malinka, Ashkan Zareie, Jan Prochazka, Radislav Sedlacek, Vendula Novosadova
Summary: Aligning and combining individually preprocessed batches in large-scale multi-batch experiments is a challenging task. We present two methods and demonstrate that retention order swaps are not rare in untargeted LC-MS data.
Article
Environmental Sciences
Shiyuan Zhao, Haitao Zhong, Chunmei Geng, Hongjia Xue, Changshui Wang, Wenxue Sun, Ruili Dang, Wenxiu Han, Pei Jiang
Summary: In this study, gas chromatography-mass spectrometry was used to investigate the toxic mechanisms of ACR in the main target tissues of rats, revealing 14 metabolic pathways related to amino acid, fatty acid, purine, and energy metabolism. The study suggests that the toxic mechanism of ACR may involve oxidative stress, inflammation, amino acid metabolism, and energy disorders.
ENVIRONMENTAL POLLUTION
(2021)
Article
Chemistry, Multidisciplinary
Parker Ladd Bremer, Gert Wohlgemuth, Oliver Fiehn
Summary: Metabolomics by GC/MS is a standardized and reliable platform for understanding small molecule biology. The West Coast Metabolomics Center at UC Davis has collated over 156,000 samples and 2000 studies into the BinBase database, which provides meaningful insight to biologists and helps standardize metabolomics studies. They have developed an easy-to-use query interface, BinDiscover, for intuitive hypothesis generation based on these metabolomic samples.
JOURNAL OF CHEMINFORMATICS
(2023)
Article
Medicine, General & Internal
Rintaro Saito, Masahiro Sugimoto, Akiyoshi Hirayama, Tomoyoshi Soga, Masaru Tomita, Toru Takebayashi
Summary: Large-scale metabolomic studies are common, but there is less focus on the reliability of uncharacterized peaks in untargeted metabolomics data. This study tested criteria to assess the reliability of uncharacterized peaks and identified some reliable peaks potentially related to important physiological processes like disease progression.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Chemistry, Analytical
Chiara Maria Vitale, Arjen Lommen, Carolin Huber, Kevin Wagner, Borja Garlito Molina, Rosalie Nijssen, Elliott James Price, Marco Blokland, Frederike van Tricht, Hans G. J. Mol, Martin Krauss, Laurent Debrauwer, Olga Pardo, Nuria Leon, Jana Klanova, Jean-Philippe Antignac
Summary: A set of QA/QC criteria for nontargeted measurement of pesticide exposure markers in human urine has been proposed and applied in the HBM4EU project. The criteria include monitoring signal intensities, mass accuracy, and retention times of selected markers. The results show high repeatability and accuracy of the data. This is the first time that harmonized QA/QC criteria have been used to assess the quality of nontargeted analysis of human samples across multiple laboratories.
ANALYTICAL CHEMISTRY
(2022)
Article
Agriculture, Dairy & Animal Science
Jieyi Qin, Qingqing Cheng, Ziyu Cai, Lin Zhang, Tong Xing, Xinglian Xu, Feng Gao
Summary: The aim of this study was to identify biomarkers for the diagnosis of wooden breast (WB) myopathy in male broilers by characterizing the serum metabolic profiles using metabolomics analysis. A clear separation was observed between normal (CON) and WB groups based on the analysis of 73 significantly different metabolites. Nine significantly altered metabolites were identified as excellent discriminant biomarkers for WB myopathy. This study provides new insights into the pathogenesis of WB and offers potential biomarkers for diagnostic purposes.
Article
Nutrition & Dietetics
Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer, Bernhard Kuster
Summary: Plants are crucial for sustainable global food supply, but the understanding of crop proteomes is limited. The presence of secondary metabolites in crop plants has hindered proteomic analyses, requiring individually optimized protein extraction protocols. In this study, a universal protein extraction protocol combined with an automated SP3 protocol and optimized micro-LC-MS/MS conditions was developed for high-quality proteomic analysis of crop plants. The workflow was successfully applied to analyze the proteomes of mature tomato fruits, demonstrating its robustness and potential for large-scale projects mapping crop tissue proteomes.
Article
Biochemistry & Molecular Biology
Miriam Hoene, Xinjie Zhao, Juergen Machann, Andreas L. L. Birkenfeld, Martin Heni, Andreas Peter, Andreas Niess, Anja Moller, Rainer Lehmann, Guowang Xu, Cora Weigert
Summary: Physical exercise is a powerful preventative measure for cardiometabolic diseases. The individual response to lifestyle interventions varies and cannot currently be predicted. Recent research has shown that Lac-Phe produced during exercise could contribute to weight loss and potentially explain differences in the effectiveness of exercise interventions in humans.
Article
Medical Laboratory Technology
Disheng Feng, Zixuan Wang, Hang Li, Xianzhe Shi, Lin Zou, Hongwei Kong, Zhiliang Xu, Chaowen Yu, Chunxiu Hu, Guowang Xu
Summary: This study developed a highly efficient method for rapid and accurate measurement of 17-alpha-hydroxyprogesterone (17-OHP) and related steroids in amount/volume-limited clinic samples, which is of great importance for the precise newborn diagnosis of congenital adrenal hyperplasia (CAH) and its subtypes in clinic.
CLINICA CHIMICA ACTA
(2023)
Article
Engineering, Environmental
Chang Wang, Huayu Fu, Jun Yang, Lei Liu, Fenghong Zhang, Chunyu Yang, Hongyuan Li, Jiamiao Chen, Qi Li, Xiaolin Wang, Yaorui Ye, Nan Sheng, Yong Guo, Jiayin Dai, Guowang Xu, Xinyu Liu, Jianshe Wang
Summary: A study found that PFECAs have inhibitory effects on cellular stress signals and lead to hepatomegaly in mice. Additionally, PFECAs also have inhibitory effects on glucocorticoid receptors, which may result in extensive suppression of stress signals. Unlike other similar substances, the next-generation replacements of legacy PFASs, PFECAs, may pose potential risks to human health.
JOURNAL OF HAZARDOUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Qingqing Wang, Miriam Hoene, Chunxiu Hu, Louise Fritsche, Robert Ahrends, Gerhard Liebisch, Kim Ekroos, Andreas Fritsche, Andreas L. Birkenfeld, Xinyu Liu, Xinjie Zhao, Qi Li, Benzhe Su, Andreas Peter, Guowang Xu, Rainer Lehmann
Summary: Reliability, robustness, and interlaboratory comparability of quantitative measurements in clinical lipidomics studies are crucial. The different ex vivo stability of lipids in blood poses a risk to data interpretation. Clear recommendations for blood sample collection are necessary. In this study, we used UHPLC-high resolution mass spectrometry to investigate the stability of 417 lipid species in EDTA whole blood under different temperature conditions and time points. Our data suggest that cooling whole blood immediately and continuously, and separating plasma within 4 hours, unless focusing on robust lipids, are recommended. Lists of lipids' ex vivo (in)stability and potential biomarkers in whole blood are provided. Overall, our results contribute to the international efforts in achieving reliable and comparable clinical lipidomics studies in the future.
JOURNAL OF LIPID RESEARCH
(2023)
Article
Chemistry, Analytical
Xingyu Guo, Lina Zhou, Yi Wang, Feng Suo, Chuanxia Wang, Wei Zhou, Lingshan Gou, Maosheng Gu, Guowang Xu
Summary: This study developed a LC-MS-based method for neonatal metabolomics analysis of DBS and investigated the influences of blood volume and chromatographic effects on metabolite levels. The method showed good repeatability, precision, and linearity, and was applied to study metabolic disruptions of congenital hypothyroidism.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Biochemical Research Methods
Xin Lu, Peng Dou, Chao Li, Fujian Zheng, Lina Zhou, Xiaoyu Xie, Zixuan Wang, Guowang Xu
Summary: This study proposes an annotation strategy involving the derivatization of dipeptides and tripeptides via dansylation, which can choose dipeptides/ tripeptides using a small number of standards. A total of 198 dipeptides and 149 tripeptides were annotated, and the variations in serum dipeptides/tripeptides of three different liver diseases were characterized.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Neurosciences
Xiaojiao Xu, Qiu Yang, Zheyi Liu, Rong Zhang, Hang Yu, Manli Wang, Sheng Chen, Guowang Xu, Yaping Shao, Weidong Le
Summary: This study aimed to investigate the molecular changes at both metabolic and proteomic levels during the longitudinal progression of ALS and identify the most critical metabolic pathways and underlying mechanisms involved in ALS pathophysiological changes. The study found differential expressions of metabolites involved in purine metabolism, methionine cycle, and glycolysis in ALS mice, and abnormal expressions of enzymes in these metabolic pathways were also confirmed. Additionally, fatty acid metabolism, TCA cycle, arginine and proline metabolism, and folate-mediated one-carbon metabolism were significantly altered in this disease. The identified differential metabolites and proteins could complement existing data on metabolic reprogramming in ALS and provide new insights into the pathological mechanisms and therapeutic targets of ALS.
NEUROBIOLOGY OF DISEASE
(2023)
Article
Biochemistry & Molecular Biology
Xiaoshan Sun, Zhen Jia, Yuqing Zhang, Xinjie Zhao, Chunxia Zhao, Xin Lu, Guowang Xu
Summary: Direct infusion nanoelectrospray high-resolution mass spectrometry (DI-nESI-HRMS) is a promising tool for high-throughput metabolomics analysis. To overcome the limitations of metabolite assignment, a serum metabolome characterization method using a reaction network combined with mass accuracy and isotopic patterns filter was proposed. The approach was validated and compared to database search, showing improved coverage and accuracy rates. The method was then applied to a case study in diabetes metabolomics.
Article
Nanoscience & Nanotechnology
Ruibin Qiang, Haofei Huang, Jia Chen, Xianzhe Shi, Zengjie Fan, Guowang Xu, Hongdeng Qiu
Summary: Rheumatoid arthritis (RA) is characterized by inflammation and pain in the joints, caused in part by a lack of lubrication and excessive proinflammatory proteins. Researchers have developed two potential nanoagents, derived from herbal medicine, that offer both improved joint lubrication and anti-inflammatory effects, showing promise for treating RA.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Analytical
Xiaoshan Sun, Yueyi Xia, Xinjie Zhao, Xinxin Wang, Yuqing Zhang, Zhen Jia, Fujian Zheng, Zaifang Li, Xiuqiong Zhang, Chunxia Zhao, Xin Lu, Guowang Xu
Summary: Direct-infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FTICR MS) is a promising method for metabolomic analysis with ultrahigh mass accuracy and resolution. In this study, a novel deep characterization approach of serum metabolome was proposed using a segment-optimized spectral-stitching DI-FTICR MS method. This method combines high-confidence and database-independent formula assignments to achieve highly efficient acquisition and accurate assignment of thousands of features in a pooled human serum sample.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Xinxin Wang, Chao Li, Zaifang Li, Yanpeng Qi, Xiuqiong Zhang, Xinjie Zhao, Chunxia Zhao, Xiaohui Lin, Xin Lu, Guowang Xu
Summary: In this study, a structure-guided molecular network strategy (SGMNS) is proposed for deep annotation of untargeted metabolomics data. The strategy utilizes a global connectivity molecular network (GCMN) constructed based on molecular fingerprint similarity of chemical structures in metabolome databases. SGMNS performs network annotation propagation using known metabolites as seeds and achieves high annotation accuracy and precision.
ANALYTICAL CHEMISTRY
(2023)
Article
Environmental Sciences
Yuting Wang, Lina Zhou, Tiantian Chen, Lei You, Xianzhe Shi, Xinyu Liu, Sijia Zheng, Jie Jiang, Yuebin Ke, Guowang Xu
Summary: In this study, a 2D-LC-HRMS-based screening strategy was developed for simultaneously screening pesticides, veterinary/human drugs, and other chemical pollutants in serum. The method was validated to detect 92% and 81% of 1022 residues spiked in serum at concentrations of 50 ng/mL and 5 ng/mL, respectively. This strategy is helpful for studying the effect of exogenous exposures on human health.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemical Research Methods
Xiaoyu Xie, Liangqiang Chen, Tiantian Chen, Fan Yang, Zixuan Wang, Yang Hu, Jianjun Lu, Xin Lu, Qi Li, Xiuqiong Zhang, Ming Ma, Li Wang, Chunxiu Hu, Guowang Xu
Summary: This study presents a chlorine isotope labeling-assisted ultrahigh-performance liquid chromatography-high resolution mass spectrometry-based method for profiling and annotating carbonyl compounds in sauce flavored-Baijiu Daqu. A total of 487 carbonyl compounds were detected, among which 314 (64.5%) were positively or putatively identified. The method provides an effective and economical strategy for comprehensive analysis of carbonyl compounds in complex matrix samples.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Immunology
Xinyu Liu, Congshu Xiao, Pengwei Guan, Qianqian Chen, Lei You, Hongwei Kong, Wangshu Qin, Peng Dou, Qi Li, Yanju Li, Ying Jiao, Zhiwei Zhong, Jun Yang, Xiaolin Wang, Qingqing Wang, Jinhui Zhao, Zhiliang Xu, Hong Zhang, Rongkuan Li, Peng Gao, Guowang Xu
Summary: To control the COVID-19 pandemic, efforts have been made to achieve herd immunity through vaccination since 2020. Unfortunately, most COVID-19 vaccines were approved without a thorough evaluation process. Metabolomic analysis can authentically assess the effects of vaccines by reflecting the responses to stimuli.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Gastroenterology & Hepatology
Runze Ouyang, Juan Ding, Yan Huang, Fujian Zheng, Sijia Zheng, Yaorui Ye, Qi Li, Xiaolin Wang, Xiao Ma, Yuxin Zou, Rong Chen, Zhihong Zhuo, Zhen Li, Qi Xin, Lina Zhou, Xin Lu, Zhigang Ren, Xinyu Liu, Petia Kovatcheva-Datchary, Guowang Xu
Summary: The gut microbiota plays a crucial role in maintaining host wellbeing by producing various metabolites. The assembly of the gut microbiome is influenced by postnatal factors, but little is known about the development of the gut metabolome. Our study reveals that geography has a significant impact on microbiome dynamics in the first year of life, with major compositional differences observed between Chinese and Swedish cohorts. We found that lipid metabolism, especially acylcarnitines and bile acids, is the most abundant metabolic pathway in the newborn gut, and delivery mode and feeding contribute to differences in the gut metabolome since birth.