Article
Chemistry, Applied
Wen-qiang Cai, Cai-yan Jiang, Shan Shang, Shu-chen Wang, Kai-yue Zhu, Xiu-ping Dong, Da-yong Zhou, Peng-fei Jiang
Summary: Sea urchin gonads have high nutritional value and suffer from rapid degeneration during storage. This study aims to identify biochemical indicators for assessing the freshness of sea urchin gonads. The dominant genera and metabolites of sea urchin gonads were found to change, with specific metabolic pathways enriched in different types of metabolites. The growth of the dominant genus Aliivibrio significantly influenced the production of differential metabolites. These findings provide valuable information for accurately determining the freshness and shelf life of sea urchin gonads.
Article
Chemistry, Analytical
Xiaoling Su, Deying Chen, Liang Li, Lanjuan Li
Summary: The study demonstrates that perfusion can significantly alter the liver metabolome, recommending the use of non-perfused liver for comprehensive liver metabolomics analysis for high coverage.
ANALYTICA CHIMICA ACTA
(2021)
Article
Agriculture, Multidisciplinary
Zhihua Li, Ling Dong, Chi Zhao, Fengju Zhang, Shuang Zhao, Jingjing Zhan, Jia Li, Liang Li
Summary: This study presents a four-channel chemical isotope labeling (CIL) LC-MS approach for comprehensive metabolome analysis of high-salt fermented food. The method allows for high coverage identification and quantification of metabolites, revealing the high metabolic diversity in these foods.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Antonia Henne, Anna Vigh, Andre Maertens, Yannic Nonnenmacher, Melanie Ohm, Shirin Hosseini, Tushar H. More, Mario A. Lauterbach, Hendrikus Garritsen, Martin Korte, Wei He, Karsten Hiller
Summary: The SiMeEx method is a simplified metabolite extraction method that allows for efficient and rapid extraction of metabolites from adherent mammalian cells without the need for cell scraping. It has advantages in both time and resource efficiency, as well as applicability in high-throughput studies.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xian Luo, Liang Li
Summary: Cellular metabolomics provides insights into metabolic processes in cells, and this study investigates the effects of solvent evaporation equipment and storage conditions on high-coverage cellular metabolomics analysis. The choice of solvent evaporation equipment does not significantly impact the cellular metabolome, but the presence of methanol during storage can lead to notable changes in the metabolome after 7 days. Thoroughly drying cell samples before storage or shipment at room temperature is recommended to ensure high-quality results.
Article
Agriculture, Multidisciplinary
Bo-Min Kim, Hyeon-Jeong Lee, Yeong H. Song, Hyun-Jin Kim
Summary: Increasing NaCl concentration led to decreased growth and mineral imbalance in spinach plants. NaCl irrigation resulted in decreased levels of most metabolites, affecting the nutritional quality of spinach.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
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
Chemistry, Applied
Mengyu Chen, Wenjie Huang, Zhibin Yin, Wenyang Zhang, Qian Kong, Shaowen Wu, Wenyan Li, Zhao Bai, Alisdair R. Fernie, Xiaodan Huang, Shijuan Yan
Summary: The research found metabolic differences among black wolfberry fruits grown in different geographical regions, with some samples showing significantly different metabolite profiles with higher levels of beneficial components, providing a new direction for further studies on the health benefits of black wolfberry fruits.
Article
Cell Biology
Chandranayaka Siddaiah, Anil Kumar BM, Saligrama Adavigowda Deepak, Syed Salman Lateef, Saurabh Nagpal, Kanchugarakoppal S. Rangappa, Chakrabhavi D. Mohan, Shobith Rangappa, Madan S. Kumar, Minaxi Sharma, Vijai Kumar Gupta
Summary: This study focused on metabolite profiling and identification from the bark of Alangium salviifolium by using organic and aqueous solvents. Eighty-one secondary metabolites with therapeutic potential were identified, showcasing the therapeutic value of this plant.
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)
Article
Chemistry, Analytical
Yan-Qing Chen, Hong Shen, Ru-Jie Yang, Jian-Bo Wan
Summary: A sensitive method was developed to accurately determine 20 NAEs in biological samples by chemical isotope labeling strategy coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Derivatized NAEs provided stable and abundant specific product ions in MS/MS spectrum for quantitation, enhancing detection sensitivity by 6- to 170-fold compared to non-derivatized NAEs. The method was successfully applied to determine NAEs in serum samples and liver tissues, showing practicability in analyzing endogenous NAE in biological samples.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemistry & Molecular Biology
Rui Bai, Xiaohui Dai, Xingang Miao, Bing Xie, Feng Yu, Bin Cong, Di Wen, Chunling Ma
Summary: Diagnosing the cause of fatal intoxication by antipsychotic agents is an important task in forensic practice. In this study, liquid chromatography-mass spectrometry-based integrated metabolomics analysis was used to analyze the metabolic profiles in plasma of mice who died from fatal intoxication by chlorpromazine (CPZ) or olanzapine (OLA). A stable discriminative classification model was constructed and revealed perturbations in metabolic pathways related to fatal intoxication by CPZ/OLA. The findings suggest that metabolomics analysis can be used to explore metabolic alterations during fatal intoxication and provide evidence for the cause of death.
Article
Agronomy
Ni Zhang, Weiwen Tan, Guimei Luo, Tianyi Pu, Jinqiu Wang, Xianhu Zhang, Yuehua Song
Summary: Camellia tetracocca, a unique tea species in southwest China, is frequently attacked by the pest Empoasca onukii. The metabolic mechanisms of C. tetracocca's defense against this pest are still unclear. Through comparative analysis using GC-MS and LC-MS, differential metabolites were identified, showing that accumulation of specialized metabolites may contribute to the resistance of C. tetracocca against E. onukii. These specialized metabolites have the potential to be used as biocontrol agents against the pest.
Article
Biochemistry & Molecular Biology
Jane L. Buchanan, Jovan Tormes Vaquerano, Eric B. Taylor
Summary: This study investigated the effects of different freezing and thawing methods on mouse plasma metabolite levels. Snap-freezing with liquid nitrogen (LN2) and quick-thawing with water were found to minimize changes in metabolite levels, while freezing at -20 degrees C resulted in the most changes. The findings highlight the importance of maintaining metabolomic stability in plasma samples.
Article
Chemistry, Applied
Kun Li, Baoshan Tang, Wenwen Zhang, Xinghao Tu, Jinju Ma, Shujie Xing, Ying Shao, Jing Zhu, Fuhou Lei, Hong Zhang
Summary: In this study, an authentication method was established to detect shellac resin in shellac-based edible coatings. By identifying 13 targeted metabolites, the authentication of shellac resin was successfully performed. The feasibility of this method was verified in commercial samples, providing a scientific basis for the qualitative authentication of shellac resin.
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)