Article
Immunology
Emma Leacy, Isabella Batten, Laetitia Sanelli, Matthew McElheron, Gareth Brady, Mark A. A. Little, Hania Khouri
Summary: Immunometabolism explores the relationship between immune cell function and metabolism, and dysregulation of immune cell metabolism is a well-established feature of innate immune cell activation. This study utilized different sample preparation techniques and data normalization methods to analyze the metabolomic profiling of human monocytes. The results revealed broad and profound changes in monocyte metabolism in response to LPS stimulation, including increased cytokine production.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Jonas Rodriguez, Lina Gomez-Cano, Erich Grotewold, Natalia de Leon
Summary: This article discusses the importance of liquid chromatography-mass spectroscopy (LC-MS) in biological research and the challenges posed by technical errors. A new approach called pseudoDrift is proposed to detect and correct these errors, with demonstrated effectiveness and flexibility through data simulation. The analysis of a phenolic compound dataset from non-transgenic maize inbred lines showcases the application of this method in studying the dynamics of specialized metabolism in plants.
Article
Biochemical Research Methods
Kirsten E. E. Overdahl, Justin B. B. Collier, Anton M. M. Jetten, Alan K. K. Jarmusch
Summary: Feature finding is a common method in processing untargeted mass spectrometry data to obtain a list of chemicals present in a sample. This study introduces signal response evaluation as a method to assess the individual features observed in untargeted MS data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Food Science & Technology
Pufan Zheng, Mei Zhang, Xin Fang, Lili Tang, Zhixue Wang, Fuchen Shi
Summary: This study identified and quantified metabolites in three pear species using a targeted LC-MS/MS approach. The results showed distinct differences in metabolite composition between cultivars, and identified metabolic pathways related to fruit quality. D-xylose, formononetin, procyanidin A1 and beta-nicotinamide mononucleotide were identified as major differentially expressed metabolites.
Article
Chemistry, Analytical
Huaxu Yu, Ying Chen, Tao Huan
Summary: This study explores how experimental factors contribute to computational variation in untargeted metabolomics, proposing a quality control sample-based correction workflow to minimize this variation. The bioinformatic solution is successfully demonstrated in a metabolomic comparison of leukemia patients before and after chemotherapy, showing significant changes in metabolic features.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Zhaoxin Li, Yunlong Cheng, Jinxin Chen, Weijun Xu, Wentao Ma, Sheng Li, Erxia Du
Summary: Insect metabolites are essential for regulating the physiology, behavior, and adaptations of insects, but the systematic metabolomics within insects remains unclear. This study used HPLC-MS/MS technology to perform a comprehensive metabolomics analysis and constructed an integrated metabolic database of nine insect species with different metamorphosis types. A total of 1442 metabolites were identified, including amino acids, organic acids, fatty acids, glycerophospholipids, nucleotides, and benzene derivatives. The metabolites were enriched in important pathways related to arachidonic acid metabolism, tyrosine metabolism, phenylalanine metabolism, and insect hormone biosynthesis. The study revealed a correlation between the evolutionary relationships of species and the types of metabolites present, while the quantities of metabolites varied greatly among species. The metabolome of these representative insects provides a valuable platform for studying insect systemic metabolites and biological events at the metabolic level.
Article
Biochemical Research Methods
Ryan A. Groves, Carly C. Y. Chan, Spencer D. Wildman, Daniel B. Gregson, Thomas Rydzak, Ian A. Lewis
Summary: Liquid chromatography mass spectrometry (LC-MS) is a widely used strategy for metabolomics analyses, offering the potential for both biomarker discovery and clinical diagnostics. However, clinical applications of LC-MS require higher throughput, which has been limited by chromatographic gradient lengths. To address this issue, researchers have developed a new analytical strategy called sequential quantification using isotope dilution (SQUID), which enables high-throughput quantification of target biomarkers in complex samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Food Science & Technology
David Schuetz, Elisabeth Achten, Marina Creydt, Janet Riedl, Markus Fischer
Summary: This study used metabolomics combined with the Random Forest algorithm to trace back the geographical origin of 151 maize samples from seven countries, successfully classifying 90.5% of samples using 20 selected markers. The research suggests a high potential of the non-polar metabolome in identifying the geographic origin of maize samples.
Article
Chemistry, Applied
Lei Ye, Bo Zhang, Jie Zhou, Xiaoping Zhang, Wei Tan, Xiaolin Li
Summary: This study investigates the metabolic profiles of Auricularia cornea grown on pinecone substrates, revealing a rich variety of amino acid metabolites and significant differences related to protein synthesis. The findings contribute valuable insights into the nutritional and medicinal properties of A. cornea grown on a pinecone substrate.
Article
Biochemistry & Molecular Biology
Alex Gomez-Gomez, Paula Aguilera, Klaus Langohr, Gregori Casals, Cristina Pavon, Josep Marcos, Jordi To-Figueras, Oscar J. Pozo
Summary: Acute intermittent porphyria (AIP) is a rare inherited hepatic disorder. This study explored the metabolome of symptomatic AIP patients using advanced mass spectrometry technology. The results showed significant changes in the metabolome, particularly in the tryptophan/kynurenine pathway and tricarboxylic acid cycle.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Applied
Wenliang Wu, Meiling Lu, Jiakun Peng, Haipeng Lv, Jiang Shi, Shuguang Zhang, Zhen Liu, Jihua Duan, Dan Chen, Weidong Dai, Zhi Lin
Summary: This study investigated the chemical characteristics of Jianghua Kucha (JHKC), a special tea germplasm in China, and found that it mainly contains high levels of purine alkaloids and methylated flavanols, as well as low levels of flavonol glycosides. Caffeine metabolism, flavonoid biosynthesis, and flavonol and flavone biosynthesis were identified as the most differential metabolic pathways. JHKC can be a valuable resource for breeding tea cultivars with high contents of theacrine, non-epi-form flavanols, and methylated flavanols.
Article
Chemistry, Analytical
Sylvia K. Neef, Ute Hofmann, Thomas E. Muerdter, Matthias Schwab, Mathias Haag
Summary: The suitability of a capillary hydrophilic interaction chromatography (CapHILIC) -QTOF-MS system for non-targeted metabolomics was evaluated and compared with a narrow-bore hydrophilic interaction chromatography (HILIC) -QTOF-MS system. Both platforms detected a similar number of features and performed well in terms of retention time stability, analytical repeatability, and signal intensity. The use of CapHILIC increased the signal areas of all metabolites, though the signal-to-noise ratio was only improved for 50% of the metabolites. Further optimization of CapHILIC conditions improved reproducibility and signal intensity.
Article
Biochemistry & Molecular Biology
Ryo Konno, Takashi Matsui, Hiroaki Ito, Yusuke Kawashima, Makoto Itakura, Yoshio Kodera
Summary: GeLC-MS/MS method coupled with stable isotope dimethyl labeling provides high accuracy and comprehensive peptide comparisons, enabling accurate determination of peptide abundance ratio between samples, unaffected by the reproducibility of gel extraction or LC-MS procedures, thus facilitating the detection of proteolysis events.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Review
Plant Sciences
Bharti Sharma, Dinesh Kumar Yadav
Summary: This review explores the role of metabolomics and network pharmacology in validating therapeutic claims and evaluating the multi-targeted therapeutic approach of traditional Indian medicinal plants. Metabolomics is an effective technique for identifying metabolites in plant matrices. Chemometric techniques are used to validate the unique characteristics and authenticity of herbal medicines. Network pharmacology is the only option for analyzing large numbers of chemicals or metabolites and validating the multi-mechanistic and therapeutic approach of herbal medicines.
Article
Biochemical Research Methods
Samuel Bernardo-Bermejo, Jingchuan Xue, Linh Hoang, Elizabeth Billings, Bill Webb, M. Willy Honders, Sanne Venneker, Bram Heijs, Maria Castro-Puyana, Maria Luisa Marina, Erik B. van den Akker, Marieke Griffioen, Gary Siuzdak, Martin Giera, Elena Sanchez-Lopez
Summary: Analytical techniques with high sensitivity and selectivity are crucial in clinical sample analysis. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the standard method, but it is expensive. This study demonstrates that similar results can be achieved using a simpler single mass spectrometry detector combined with enhanced in-source fragmentation/annotation and correlated ion monitoring. The protocol provides step-by-step instructions for optimizing the conditions for this technique, making it broadly applicable and cost-effective for quantifying small molecules.
