Article
Food Science & Technology
Silvia Guazzotti, Cristina Pagliano, Francesco Dondero, Marcello Manfredi
Summary: This study evaluated the lipidomic profile of rice bran from the Italian rice variety, Roma, using ultra performance liquid chromatography-tandem mass spectrometry. Ethanol and methyl tert-butyl ether/methanol solvents were found to be excellent solvents for lipid extraction from rice bran, with ethanol being the most effective for triglycerides and N-acylethanolamines, and methyl tert-butyl ether/methanol being the most effective for diglycerides, phospholipids, and ceramides. Additionally, extraction with ethanol at 20 degrees C yielded similar results to extraction at 4 degrees C. Therefore, ethanol and methyl tert-butyl ether/methanol can be used to efficiently extract lipids from rice bran, contributing to the valorization of this by-product in a circular economy perspective.
Article
Endocrinology & Metabolism
Ying Ding, Yihong Jiang, Mingjiang Zhu, Qinling Zhu, Yaqiong He, Yao Lu, Yuan Wang, Jia Qi, Yifan Feng, Rong Huang, Huiyong Yin, Shengxian Li, Yun Sun
Summary: This study investigated the lipidomic profiles in follicular fluid (FF) of different phenotypes of Polycystic ovary syndrome (PCOS) and identified metabolic signatures and candidate biomarkers that provide a better understanding of the pathogenesis of PCOS.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Alex Apffel, Limian Zhao, Mark J. Sartain
Summary: This article introduces a novel solid-phase extraction method for extracting lipids from human plasma, which saves time and labor compared to traditional liquid-liquid extraction methods, and provides equivalent or better qualitative and quantitative results in terms of recovery, reproducibility, and lipidome coverage.
Review
Chemistry, Analytical
Denise Wolrab, Ondrej Peterka, Michaela Chocholouskova, Michal Holcapek
Summary: Ultrahigh-performance supercritical fluid chromatography/mass spectrometry (UHPSFC/MS) is a fast analytical method for high-throughput lipidomic analysis. It offers lipid class separation and lipid species separation modes, with fast analysis time and comparable reproducibility and sensitivity.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Tomas Cajka, Jiri Hricko, Lucie Rudl Kulhava, Michaela Paucova, Michaela Novakova, Oliver Fiehn, Ondrej Kuda
Summary: Liquid chromatography-mass spectrometry (LC-MS) is crucial for analyzing complex lipids in biological samples. The impact of organic solvent quality in LC-MS analysis is often overlooked and can affect the reliability of the data. Annotation of complex lipids is prone to biases, leading to potential misidentifications and incomplete characterization.
Article
Biochemical Research Methods
Monique J. Ryan, Alanah Grant-St James, Nathan G. Lawler, Mark W. Fear, Edward Raby, Fiona M. Wood, Garth L. Maker, Julien Wist, Elaine Holmes, Jeremy K. Nicholson, Luke Whiley, Nicola Gray
Summary: This study presents an optimized comprehensive targeted workflow for plasma and serum lipid quantification, which combines stable isotope internal standard dilution, automated sample preparation, and ultrahigh performance liquid chromatography-tandem mass spectrometry with rapid polarity switching. The method is robust to common sources of analytical variation and is suitable for large-scale, multibatch applications in precision medicine.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Evan L. Pannkuk, Nicole A. S. -Y. Dorville, Shivani Bansal, Sunil Bansal, Yvonne A. Dzal, Quinn E. Fletcher, Kaleigh J. O. Norquay, Albert J. Fornace Jr, Craig K. R. Willis
Summary: This study investigates the lipidomic changes in bats with white-nose syndrome (WNS) and suggests that oxidative stress occurs in the early stages of WNS before fat depletion, but not inflammatory response. The study compared WNS-susceptible Myotis lucifugus to WNS-resistant Eptesicus fuscus and found altered splenic lipid levels only in M. lucifugus.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Sophie Catanese, Raoul K. Khanna, Antoine Lefevre, Hugo Alarcan, Pierre-Jean Pisella, Patrick Emond, Helene Blasco
Summary: To apply metabo-lipidomics in ophthalmological and systemic diseases, it is necessary to standardize the preanalytical and analytical steps in human tears. This study compared different methods for each step of the workflow and found that methanol/water extraction provided the best results for metabolomics, while Folch extraction was superior for lipidomics. The use of microcapillary glass tube for sampling was superior to Schirmer strip for metabolomics. A volume of 5 mu L provided satisfactory metabo-lipidomic coverage. These findings will contribute to improving the metabo-lipidomic workflow in human tears for the identification of new biomarkers.
Article
Biochemistry & Molecular Biology
Nikolay Berezhnoy, Amaury Cazenave-Gassiot, Liang Gao, Juat Chin Foo, Shanshan Ji, Viduthalai Rasheedkhan Regina, Pui Khee Peggy Yap, Markus R. Wenk, Staffan Kjelleberg, Thomas William Seviour, Jamie Hinks
Summary: This study investigates the changes in lipid composition of Escherichia coli under different environmental conditions, particularly during growth phases and under stress. The researchers found that the cyclopropanation of fatty acyl chains plays a key role in lipid diversity, with a bias towards shorter chains. Additionally, the presence of ampicillin and chloramphenicol leads to an increase in saturated fatty acyl chains, affecting membrane properties and bacterial stress tolerance.
Article
Chemistry, Analytical
Dong Hao Wang, Hui Gyu Park, Zhen Wang, R. J. Scott Lacombe, Vadim V. Shmanai, Andrei Bekish, Karsten Schmidt, Mikhail S. Shchepinov, J. Thomas Brenna
Summary: This study introduces a novel method for quantitatively determining the deuterium content along a hydrocarbon chain. By utilizing deuteration reactions and analysis techniques, the method enables accurate quantification of deuterium abundance at different positions of D-HUFA.
ANALYTICAL CHEMISTRY
(2021)
Article
Geochemistry & Geophysics
Jayne E. Rattray, Alexandra Zetterlind, Rienk H. Smittenberg, Christian Potiszil, Anna Neubeck
Summary: Energy from serpentinization processes may have fueled the origin of life on Earth. Investigating biological signatures in terrestrial serpentinite-impacted environments is essential for understanding molecular signature preservation on extraterrestrial bodies. Mass spectrometry analysis of Chimaera serpentinite rocks from Turkey revealed the presence of diverse biological signatures, indicating the potential presence of different microbial communities in different rock types and locations.
ORGANIC GEOCHEMISTRY
(2022)
Article
Biochemical Research Methods
Lauren M. Bishop, Oliver Fiehn
Summary: Large-scale lipidomic analyses have been limited by the cost and accessibility of traditional venipuncture sampling. Microsampling techniques offer a less-invasive and more accessible alternative. From a single drop of blood, plasma separation cards (PSC) deliver two volumetric dried plasma samples which are studied here for profiling endogenous blood lipids.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dmitry Senko, Anna Gorovaya, Elena Stekolshchikova, Nickolay Anikanov, Artur Fedianin, Maxim Baltin, Olga Efimova, Daria Petrova, Tatyana Baltina, Mikhail A. Lebedev, Philipp Khaitovich, Anna Tkachev
Summary: The study assessed blood lipidome alterations in a rat sciatic nerve crush injury model and found delayed systematic alterations in fatty acid metabolism after nerve injury.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Bailey S. Rose, Jody C. May, Jaqueline A. Picache, Simona G. Codreanu, Stacy D. Sherrod, John A. McLean
Summary: This study presents a data processing workflow to increase confidence in molecular class annotations in lipidomics using collision cross-section (CCS) values. The workflow combines regression models and machine learning strategies to improve lipid identification and classification.
Article
Chemistry, Analytical
Christian Ieritano, J. Larry Campbell, W. Scott Hopkins
Summary: A machine learning approach was used to predict compensation voltages for ion transmission in differential mobility spectrometry (DMS) using a database of 409 cationic analytes, achieving a high level of prediction accuracy. By including lower separation voltages in the model, accuracy was further improved, especially in capturing different behavior types of ions.
Article
Biology
Chao Li, Peng Dou, Tianxiang Wang, Xin Lu, Guowang Xu, Xiaohui Lin
Summary: Studying miRNA synergy and identifying miRNA synergistic modules can help understand complex diseases such as cancers. A new method called DDRM combines knowledge databases and miRNA data to define disease-related modules and construct a weighted miRNA synergistic network. Experiments on TCGA datasets showed that DDRM can accurately distinguish cancer samples from normal samples and outperforms previous methods. Validation on prostate cancer data also demonstrated superior performance. Hence, combining miRNA synergy networks and miRNA data is significant for studying disease mechanisms.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemical Research Methods
Xiaoxiao Wang, Fujian Zheng, Meizhen Sheng, Guowang Xu, Xiaohui Lin
Summary: To improve the accuracy of retention time (RT) prediction, this study proposes a method called multi-data combinations and adaptive neural network (MDC-ANN). MDC-ANN establishes the RT prediction model for a target chromatographic system using transfer learning and a deep learning model trained on a large dataset. Experimental results demonstrate that integrating multiple molecular representations provides more information, improves RT prediction performance, and contributes to compound annotation. Different chromatographic systems may require different molecular representation combinations for accurate RT prediction. Hence, MDC-ANN, which automatically determines the best combination of molecular representations for a specific system, shows promise for accurate RT prediction in real applications.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
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)
Review
Chemistry, Analytical
Di Yu, Lina Zhou, Xinyu Liu, Guowang Xu
Summary: The introduction of stable isotope labeling (SIL) technology has become a routine tool for functional metabolomics studies and allows for a deeper understanding of dynamic metabolic regulation in organisms. Mass spectrometry (MS) techniques have shown great vitality in this field by utilizing the different mass spectrometric characteristics between endogenous metabolites and their isotope-labeling forms. Recent advances in MS-based stable isotope-resolved metabolomics (SIRM) methods have expanded the breadth and depth of SIRM research by improving sample pretreatment, MS analysis, and data analysis. This review describes the recent progress of SIRM methods, summarizes their applications in metabolite identification, accurate quantification, and metabolic flux analysis, and discusses current limitations and challenges.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(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)
Editorial Material
Chemistry, Analytical
Xinyu Liu, Xin Lu, Xianzhe Shi, Guowang Xu
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Cardiac & Cardiovascular Systems
Gaokun Qiu, Yuhui Lin, Yang Ouyang, Mingrong You, Xinjie Zhao, Hao Wang, Rundong Niu, Wending Li, Xuedan Xu, Qi Yan, Yurong Liu, Yingmei Li, Handong Yang, Xiulou Li, Meian He, Xiaomin Zhang, Xiao-Ou Shu, Guowang Xu, Tangchun Wu
Summary: This study aimed to identify metabolites associated with incident acute coronary syndrome (ACS) and explore the causality of these associations. Three metabolites were found to be associated with ACS risk, including one that is a degradation product of a gut-brain peptide, one that is a marker of short-term glycemic excursions, and one that is a very-long-chain saturated fatty acid. These findings highlight the importance of gastrointestinal hormones and glycemic fluctuations in the development of ACS.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(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.