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Song Q, Zhao Z, Liu H, Zhang J, Wang Z, Zhang Y, Ma G, Ge S. Pseudotargeted lipidomics analysis of scoparone on glycerophospholipid metabolism in non-alcoholic steatohepatitis mice by LC-MRM-MS. PeerJ 2024; 12:e17380. [PMID: 38799063 PMCID: PMC11122033 DOI: 10.7717/peerj.17380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/21/2024] [Indexed: 05/29/2024] Open
Abstract
As the inflammatory subtype of nonalcoholic fatty liver disease (NAFLD), the progression of nonalcoholic steatohepatitis (NASH) is associated with disorders of glycerophospholipid metabolism. Scoparone is the major bioactive component in Artemisia capillaris which has been widely used to treat NASH in traditional Chinese medicine. However, the underlying mechanisms of scoparone against NASH are not yet fully understood, which hinders the development of effective therapeutic agents for NASH. Given the crucial role of glycerophospholipid metabolism in NASH progression, this study aimed to characterize the differential expression of glycerophospholipids that is responsible for scoparone's pharmacological effects and assess its efficacy against NASH. Liquid chromatography-multiple reaction monitoring-mass spectrometry (LC-MRM-MS) was performed to get the concentrations of glycerophospholipids, clarify mechanisms of disease, and highlight insights into drug discovery. Additionally, pathologic findings also presented consistent changes in high-fat diet-induced NASH model, and after scoparone treatment, both the levels of glycerophospholipids and histopathology were similar to normal levels, indicating a beneficial effect during the observation time. Altogether, these results refined the insights on the mechanisms of scoparone against NASH and suggested a route to relieve NASH with glycerophospholipid metabolism. In addition, the current work demonstrated that a pseudotargeted lipidomic platform provided a novel insight into the potential mechanism of scoparone action.
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Affiliation(s)
- Qi Song
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ziyi Zhao
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
| | - Hu Liu
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
| | - Jinling Zhang
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
| | - Zhiqiang Wang
- Hebei Key Laboratory of Public Health Safety, School of Public HealthPublic Health, Hebei University, Baoding, Hebei, China
| | - Yunqi Zhang
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
| | - Guowei Ma
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
| | - Shaoqin Ge
- College of Traditional Chinese Medicine, Hebei University, Baoding, Hebei, China
- College of Basic Medical Science, Hebei University of Technology, Baoding, Hebei, China
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2
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Peña-Bautista C, Álvarez-Sánchez L, García-Lluch G, Raga L, Quevedo P, Peretó M, Balaguer A, Baquero M, Cháfer-Pericás C. Relationship between Plasma Lipid Profile and Cognitive Status in Early Alzheimer Disease. Int J Mol Sci 2024; 25:5317. [PMID: 38791355 PMCID: PMC11120743 DOI: 10.3390/ijms25105317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Alzheimer disease (AD) is a heterogeneous and complex disease in which different pathophysiological mechanisms are involved. This heterogenicity can be reflected in different atrophy patterns or clinical manifestations. Regarding biochemical pathways involved in early AD, lipid metabolism plays an important role; therefore, lipid levels have been evaluated as potential AD diagnosis biomarkers, and their levels could be related to different AD clinical manifestations. Therefore, the aim of this work is to study AD lipid profiles from early AD patients and evaluate their clinical significance. For this purpose, untargeted plasma lipidomic analysis was carried out in early AD patients (n = 31) diagnosed with cerebrospinal fluid (CSF) biomarkers. Cluster analysis was carried out to define early AD subgroups according to the lipid levels. Then, the clinical significance of each lipid profile subgroup was studied, analyzing differences for other variables (cognitive status, CSF biomarkers, medication, comorbidities, age, and gender). The cluster analysis revealed two different groups of AD patients. Cluster 1 showed higher levels of plasma lipids and better cognitive status than Cluster 2. However, no differences were found for the other variables (age, gender, medication, comorbidities, cholesterol, and triglycerides levels) between both groups. Plasma lipid levels could differentiate two early AD subgroups, which showed different cognitive statuses. However, further research with a large cohort and longitudinal study evaluating the clinical evolution of these patients is required. In general, it would involve a relevant advance in the knowledge of AD pathological mechanisms, potential treatments, and precision medicine.
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Affiliation(s)
- Carmen Peña-Bautista
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
| | - Lourdes Álvarez-Sánchez
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
| | - Gemma García-Lluch
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
| | - Luis Raga
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
| | - Paola Quevedo
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
| | - Mar Peretó
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
| | - Angel Balaguer
- Faculty of Mathematical Sciences, University of Valencia, 46100 Burjassot, Spain;
| | - Miguel Baquero
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
- Division of Neurology, Hospital Universitari I Politècnic La Fe, 46026 Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Alzheimer’s Disease Research Group, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (G.G.-L.); (L.R.); (M.P.)
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3
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Fernandez Requena B, Gonzalez-Riano C, Barbas C. Addressing the untargeted lipidomics challenge in urine samples: Comparative study of extraction methods by UHPLC-ESI-QTOF-MS. Anal Chim Acta 2024; 1299:342433. [PMID: 38499427 DOI: 10.1016/j.aca.2024.342433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Urine analysis has remained a fundamental and widely used method in clinical diagnostics for over a century. With its minimal invasive nature and comprehensive range of analytes, urine has established itself as a clinical diagnostic tool for various disorders, including renal, urological, metabolic, and endocrine diseases. Furthermore, urine's unique attributes make it an attractive matrix for biomarker discovery, as well as in assessing the metabolic and physiological states of patients and healthy individuals alike. However, limitations in our knowledge of average values and sources of urinary lipids decrease the wider clinical application of urinary lipidomics. In this context, untargeted lipidomics analysis relies heavily on the extraction and analysis of lipids in biological samples. Nevertheless, this type of analysis presents challenges in lipid identification due to the diverse nature of lipids. Therefore, proper sample treatment before analysis is crucial to obtain robust and reproducible lipidomic profiles. To address this gap, we conducted a comparative study of a urine pool sample collected from twenty healthy volunteers using four different lipid extraction methods: one biphasic and three monophasic protocols. The extracted lipids were then analyzed using UHPLC-MS and MS/MS, and the semi-quantification of all the accurately annotated lipid species was performed for each extraction method.
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Affiliation(s)
- Belen Fernandez Requena
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España
| | - Carolina Gonzalez-Riano
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España.
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4
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Lee IC, Tumanov S, Wong JW, Stocker R, Ho JW. Integrative processing of untargeted metabolomic and lipidomic data using MultiABLER. iScience 2023; 26:106881. [PMID: 37260745 PMCID: PMC10227420 DOI: 10.1016/j.isci.2023.106881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/13/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
Mass spectrometry (MS)-based untargeted metabolomic and lipidomic approaches are being used increasingly in biomedical research. The adoption and integration of these data are critical to the overall multi-omic toolkit. Recently, a sample extraction method called Multi-ABLE has been developed, which enables concurrent generation of proteomic and untargeted metabolomic and lipidomic data from a small amount of tissue. The proteomics field has a well-established set of software for processing of acquired data; however, there is a lack of a unified, off-the-shelf, ready-to-use bioinformatics pipeline that can take advantage of and prepare concurrently generated metabolomic and lipidomic data for joint downstream analyses. Here we present an R pipeline called MultiABLER as a unified and simple upstream processing and analysis pipeline for both metabolomics and lipidomics datasets acquired using liquid chromatography-tandem mass spectrometry. The code is available via an open-source license at https://github.com/holab-hku/MultiABLER.
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Affiliation(s)
- Ian C.H. Lee
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
| | - Sergey Tumanov
- Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jason W.H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Roland Stocker
- Heart Research Institute, 7 Eliza Street, Newtown, NSW 2042, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joshua W.K. Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong SAR, China
- Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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5
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Shi C, Zi Y, Huang S, Chen J, Wang X, Zhong J. Development and application of lipidomics for food research. ADVANCES IN FOOD AND NUTRITION RESEARCH 2023; 104:1-42. [PMID: 37236729 DOI: 10.1016/bs.afnr.2022.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Lipidomics is an emerging and promising omics derived from metabolomics to comprehensively analyze all of lipid molecules in biological matrices. The purpose of this chapter is to introduce the development and application of lipidomics for food research. First, three aspects of sample preparation are introduced: food sampling, lipid extraction, and transportation and storage. Second, five types of instruments for data acquisition are summarized: direct infusion-mass spectrometry (MS), chromatographic separation-MS, ion mobility-MS, MS imaging, and nuclear magnetic resonance spectroscopy. Third, data acquisition and analysis software are described for the lipidomics software development. Fourth, the application of lipidomics for food research is discussed such as food origin and adulteration analysis, food processing research, food preservation research, and food nutrition and health research. All the contents suggest that lipidomics is a powerful tool for food research based on its ability of lipid component profile analysis.
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Affiliation(s)
- Cuiping Shi
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ye Zi
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National R&D Branch Center for Freshwater Aquatic Products Processing Technology (Shanghai), Integrated Scientific Research Base on Comprehensive Utilization Technology for By-Products of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Shudan Huang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National R&D Branch Center for Freshwater Aquatic Products Processing Technology (Shanghai), Integrated Scientific Research Base on Comprehensive Utilization Technology for By-Products of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Jiahui Chen
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National R&D Branch Center for Freshwater Aquatic Products Processing Technology (Shanghai), Integrated Scientific Research Base on Comprehensive Utilization Technology for By-Products of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Xichang Wang
- National R&D Branch Center for Freshwater Aquatic Products Processing Technology (Shanghai), Integrated Scientific Research Base on Comprehensive Utilization Technology for By-Products of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Jian Zhong
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai Jiao Tong University School of Medicine, Shanghai, China; National R&D Branch Center for Freshwater Aquatic Products Processing Technology (Shanghai), Integrated Scientific Research Base on Comprehensive Utilization Technology for By-Products of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, College of Food Science & Technology, Shanghai Ocean University, Shanghai, China.
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6
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Accurate Analysis of Lipid Building Blocks Using the Tool LipidOne. Methods Mol Biol 2023; 2625:323-336. [PMID: 36653654 DOI: 10.1007/978-1-0716-2966-6_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
LC/MS-based analysis techniques combined with specialized lipid platforms allow the qualitative and quantitative determination of thousands of lipid molecules. Each individual molecule can be considered as an assembly of smaller parts, often called building blocks that are the result of a myriad of biochemical synthesis and transformation processes. LipidOne is a new lipidomic tool that automatically highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and between experimental groups. Thanks to LipidOne, the discovered differences among lipid building blocks can be easily linked to the activity of specific enzymes.
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7
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Del Prete E, Campos AM, Della Rocca F, Gallo C, Fontana A, Nuzzo G, Angelini C. ADViSELipidomics: a workflow for analyzing lipidomics data. Bioinformatics 2022; 38:5460-5462. [PMID: 36308459 PMCID: PMC9750127 DOI: 10.1093/bioinformatics/btac706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Indexed: 12/25/2022] Open
Abstract
SUMMARY ADViSELipidomics is a novel Shiny app for preprocessing, analyzing and visualizing lipidomics data. It handles the outputs from LipidSearch and LIQUID for lipid identification and quantification and the data from the Metabolomics Workbench. ADViSELipidomics extracts information by parsing lipid species (using LIPID MAPS classification) and, together with information available on the samples, performs several exploratory and statistical analyses. When the experiment includes internal lipid standards, ADViSELipidomics can normalize the data matrix, providing normalized concentration values per lipids and samples. Moreover, it identifies differentially abundant lipids in simple and complex experimental designs, dealing with batch effect correction. Finally, ADViSELipidomics has a user-friendly graphical user interface and supports an extensive series of interactive graphics. AVAILABILITY AND IMPLEMENTATION ADViSELipidomics is freely available at https://github.com/ShinyFabio/ADViSELipidomics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Fabio Della Rocca
- Institute for Calculus Applications ‘M. Picone’, CNR, 80131 Naples, Italy
| | - Carmela Gallo
- Institute of Biomolecular Chemistry, CNR, 80078 Naples, Italy
| | - Angelo Fontana
- Institute of Biomolecular Chemistry, CNR, 80078 Naples, Italy,Department of Biology, University of Naples “Federico II”, 80126 Naples, Italy
| | - Genoveffa Nuzzo
- Institute of Biomolecular Chemistry, CNR, 80078 Naples, Italy
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Lipidic profiles of patients starting peritoneal dialysis suggest an increased cardiovascular risk beyond classical dyslipidemia biomarkers. Sci Rep 2022; 12:16394. [PMID: 36180468 PMCID: PMC9525574 DOI: 10.1038/s41598-022-20757-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 09/19/2022] [Indexed: 11/15/2022] Open
Abstract
Patients on peritoneal dialysis (PD) have an increased risk of cardiovascular disease (CVD) and an atherogenic lipid profile generated by exposure to high glucose dialysis solutions. In the general population, the reduction of classic lipids biomarkers is associated with improved clinical outcomes; however, the same results have not been seen in PD population, a lack of data this study aims to fulfill. Single-center prospective observational study of a cohort of CKD patients who started renal replacement therapy with continuous ambulatory peritoneal dialysis. The differences in the lipid profile and analytical variables before and 6 months after the start of peritoneal dialysis were analyzed. Samples were analyzed on an Ultra-Performance Liquid Chromatography system. Thirty-nine patients were enrolled in this study. Their mean age was 57.9 ± 16.3 years. A total of 157 endogenous lipid species of 11 lipid subclasses were identified. There were significant increases in total free fatty acids (p < 0.05), diacylglycerides (p < 0.01), triacylglycerides, (p < 0.01), phosphatidylcholines (p < 0.01), phosphatidylethanolamines (p < 0.01), ceramides (p < 0.01), sphingomyelins (p < 0.01), and cholesterol esters (p < 0.01) from baseline to 6 months. However, there were no differences in the classical lipid markers, neither lysophosphatidylcholines, monoacylglycerides, and sphingosine levels. 6 months after the start of the technique, PD patients present changes in the lipidomic profile beyond the classic markers of dyslipidemia.
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9
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Peña-Bautista C, Álvarez-Sánchez L, Roca M, García-Vallés L, Baquero M, Cháfer-Pericás C. Plasma Lipidomics Approach in Early and Specific Alzheimer’s Disease Diagnosis. J Clin Med 2022; 11:jcm11175030. [PMID: 36078960 PMCID: PMC9457360 DOI: 10.3390/jcm11175030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Background: The brain is rich in lipid content, so a physiopathological pathway in Alzheimer’s disease (AD) could be related to lipid metabolism impairment. The study of lipid profiles in plasma samples could help in the identification of early AD changes and new potential biomarkers. Methods: An untargeted lipidomic analysis was carried out in plasma samples from preclinical AD (n = 11), mild cognitive impairment-AD (MCI-AD) (n = 31), and healthy (n = 20) participants. Variables were identified by means of two complementary methods, and lipid families’ profiles were studied. Then, a targeted analysis was carried out for some identified lipids. Results: Statistically significant differences were obtained for the diglycerol (DG), lysophosphatidylethanolamine (LPE), lysophosphatidylcholine (LPC), monoglyceride (MG), and sphingomyelin (SM) families as well as for monounsaturated (MUFAs) lipids, among the participant groups. In addition, statistically significant differences in the levels of lipid families (ceramides (Cer), LPE, LPC, MG, and SM) were observed between the preclinical AD and healthy groups, while statistically significant differences in the levels of DG, MG, and PE were observed between the MCI-AD and healthy groups. In addition, 18:1 LPE showed statistically significant differences in the targeted analysis between early AD (preclinical and MCI) and healthy participants. Conclusion: The different plasma lipid profiles could be useful in the early and minimally invasive detection of AD. Among the lipid families, relevant results were obtained from DGs, LPEs, LPCs, MGs, and SMs. Specifically, MGs could be potentially useful in AD detection; while LPEs, LPCs, and SM seem to be more related to the preclinical stage, while DGs are more related to the MCI stage. Specifically, 18:1 LPE showed a potential utility as an AD biomarker.
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Affiliation(s)
- Carmen Peña-Bautista
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Lourdes Álvarez-Sánchez
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Marta Roca
- Analytical Unit, Health Research Institute La Fe, 46026 Valencia, Spain
| | - Lorena García-Vallés
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Miguel Baquero
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain
- Correspondence:
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10
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Alcoriza-Balaguer MI, García-Cañaveras JC, Ripoll-Esteve FJ, Roca M, Lahoz A. LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation. Bioinformatics 2022; 38:4826-4828. [PMID: 36005855 DOI: 10.1093/bioinformatics/btac581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION LipidMS was initially envisioned to use fragmentation rules and data-independent acquisition (DIA) for lipid annotation. However, data-dependent acquisition (DDA) remains the most widespread acquisition mode for untargeted LC-MS/MS-based lipidomics. Here we present LipidMS 3.0, an R package that not only adds DDA and new lipid classes to its pipeline, but also the required functionalities to cover the whole data analysis workflow from pre-processing (i.e., peak-peaking, alignment and grouping) to lipid annotation. RESULTS We applied the new workflow in the data analysis of a commercial human serum pool spiked with 68 representative lipid standards acquired in full scan, DDA and DIA modes. When focusing on the detected lipid standard features and total identified lipids, LipidMS 3.0 data pre-processing performance is similar to XCMS, whereas it complements the annotations returned by MS-DIAL, providing a higher level of structural information and a lower number of incorrect annotations. To extend and facilitate LipidMS 3.0 usage among less experienced R-programming users, the workflow was also implemented as a web-based application. AVAILABILITY The LipidMS R-package is freely available at https://CRAN.R-project.org/package=LipidMS and as a website at http://www.lipidms.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- María Isabel Alcoriza-Balaguer
- Biomarkers and Precision Medicine Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Juan Carlos García-Cañaveras
- Biomarkers and Precision Medicine Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Francisco Javier Ripoll-Esteve
- Department of Informatics, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Marta Roca
- Analytical Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026
| | - Agustín Lahoz
- Biomarkers and Precision Medicine Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain.,Analytical Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026
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11
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Anh NH, Yoon YC, Min YJ, Long NP, Jung CW, Kim SJ, Kim SW, Lee EG, Wang D, Wang X, Kwon SW. Caenorhabditis elegans deep lipidome profiling by using integrative mass spectrometry acquisitions reveals significantly altered lipid networks. J Pharm Anal 2022; 12:743-754. [PMID: 36320604 PMCID: PMC9615529 DOI: 10.1016/j.jpha.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 12/02/2022] Open
Abstract
Lipidomics coverage improvement is essential for functional lipid and pathway construction. A powerful approach to discovering organism lipidome is to combine various data acquisitions, such as full scan mass spectrometry (full MS), data-dependent acquisition (DDA), and data-independent acquisition (DIA). Caenorhabditis elegans (C. elegans) is a useful model for discovering toxic-induced metabolism, high-throughput drug screening, and a variety of human disease pathways. To determine the lipidome of C. elegans and investigate lipid disruption from the molecular level to the system biology level, we used integrative data acquisition. The methyl-tert-butyl ether method was used to extract L4 stage C. elegans after exposure to triclosan (TCS), perfluorooctanoic acid, and nanopolystyrene (nPS). Full MS, DDA, and DIA integrations were performed to comprehensively profile the C. elegans lipidome by Q-Exactive Plus MS. All annotated lipids were then analyzed using lipid ontology and pathway analysis. We annotated up to 940 lipids from 20 lipid classes involved in various functions and pathways. The biological investigations revealed that when C. elegans were exposed to nPS, lipid droplets were disrupted, whereas plasma membrane-functionalized lipids were likely to be changed in the TCS treatment group. The nPS treatment caused a significant disruption in lipid storage. Triacylglycerol, glycerophospholipid, and ether class lipids were those primarily hindered by toxicants. Finally, toxicant exposure frequently involved numerous lipid-related pathways, including the phosphoinositide 3-kinase/protein kinase B pathway. In conclusion, an integrative data acquisition strategy was used to characterize the C. elegans lipidome, providing valuable biological insights into hypothesis generation and validation. Multiple data acquisitions were used to profile the lipidome of C. elegans. 940 detected lipids of 20 main classes involved in various pathways. Relevant hypotheses were generated using high-coverable lipidomics and pathways analysis.
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12
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Pellegrino RM, Giulietti M, Alabed HBR, Buratta S, Urbanelli L, Piva F, Emiliani C. LipidOne: user-friendly lipidomic data analysis tool for a deeper interpretation in a systems biology scenario. Bioinformatics 2022; 38:1767-1769. [PMID: 34971364 DOI: 10.1093/bioinformatics/btab867] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/27/2021] [Accepted: 12/27/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY LC/MS-based analysis techniques combined with specialized lipid tool allow for the qualitative and quantitative determination of thousands of lipid molecules. Some recent bioinformatics tools have been developed to study changes in the lipid profile in case-control experiments and correlate these changes to different enzyme activity or gene expression. However, the existing tools have the limitation to treat only the assembled lipid molecules. In reality, each individual molecule can be considered as an assembly of smaller parts, often called building blocks. These are the result of a myriad of biochemical synthesis and transformation processes that, from a systems biology perspective, should not be ignored. Here, we present LipidOne, a new lipidomic tool which highlights all qualitative and quantitative changes in lipid building blocks both among all detected lipid classes and among experimental groups. Thanks to LipidOne, even differences in lipid building blocks can now be linked to the activity of specific classes of enzymes, transcripts and genes. AVAILABILITY AND IMPLEMENTATION LipidOne software is freely available at www.dcbb.unipg.it/LipidOne and https://github.com/matteogiulietti/LipidOne. CONTACT roberto.pellegrino@unipg.it. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60020 Ancona, Italy
| | - Husam B R Alabed
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06100 Perugia, Italy
| | - Sandra Buratta
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06100 Perugia, Italy
| | - Lorena Urbanelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06100 Perugia, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60020 Ancona, Italy
| | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06100 Perugia, Italy
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13
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Song Y, Cai C, Song Y, Sun X, Liu B, Xue P, Zhu M, Chai W, Wang Y, Wang C, Li M. A Comprehensive Review of Lipidomics and Its Application to Assess Food Obtained from Farm Animals. Food Sci Anim Resour 2022; 42:1-17. [PMID: 35028570 PMCID: PMC8728500 DOI: 10.5851/kosfa.2021.e59] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 12/04/2022] Open
Abstract
Lipids are one of the major macronutrients essential for adequate growth and
maintenance of human health. Their structure is not only complex but also
diverse, which makes systematic and holistic analyses challenging; consequently,
little is known regarding the relationship between phenotype and mechanism of
action. In recent years, rapid advancements have been made in the fields of
lipidomics and bioinformatics. In comparison with traditional approaches, mass
spectrometry-based lipidomics can rapidly identify as well as quantify
>1,000 lipid species at the same time, facilitating comprehensive, robust
analyses of lipids in tissues, cells, and body fluids. Accordingly, lipidomics
is now being widely applied in various fields, particularly food and nutrition
science. In this review, we discuss lipid classification, extraction techniques,
and detection and analysis using lipidomics. We also cover how lipidomics is
being used to assess food obtained from livestock and poultry. The information
included herein should serve as a reference to determine how to characterize
lipids in animal food samples, enhancing our understanding of the application of
lipidomics in the field in animal husbandry.
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Affiliation(s)
- Yinghua Song
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Changyun Cai
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Yingzi Song
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Xue Sun
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Baoxiu Liu
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Peng Xue
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Mingxia Zhu
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Wenqiong Chai
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Yonghui Wang
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Changfa Wang
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
| | - Mengmeng Li
- College of Agronomy, Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng 252059, China
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14
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Kehelpannala C, Rupasinghe T, Hennessy T, Bradley D, Ebert B, Roessner U. The state of the art in plant lipidomics. Mol Omics 2021; 17:894-910. [PMID: 34699583 DOI: 10.1039/d1mo00196e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipids are a group of compounds with diverse structures that perform several important functions in plants. To unravel and better understand their in vivo functions, plant biologists have been using various lipidomic technologies including liquid-chromatography (LC)-mass spectrometry (MS). However, there are still significant challenges in LC-MS based plant lipidomics, which need to be addressed. In this review, we provide an overview of the key developments in LC-MS based lipidomic approaches to detect and identify plant lipids with emphasis on areas that can be further improved. Given that the cellular lipidome is estimated to contain hundreds of thousands of lipids,1,2 many of the lipid structures remain to be discovered. Furthermore, the plant lipidome is considered to be significantly more complex compared to that of mammals. Recent technical developments in mass spectrometry have made the detection of novel lipids possible; hence, approaches that can be used for plant lipid discovery are also discussed.
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Affiliation(s)
- Cheka Kehelpannala
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | | | - Thomas Hennessy
- Agilent Technologies Australia Pty Ltd, 679 Springvale Road, Mulgrave, VIC 3170, Australia
| | - David Bradley
- Agilent Technologies Australia Pty Ltd, 679 Springvale Road, Mulgrave, VIC 3170, Australia
| | - Berit Ebert
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Ute Roessner
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia.
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15
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Tapia A, Palomino-Schätzlein M, Roca M, Lahoz A, Pineda-Lucena A, López del Amo V, Galindo MI. Mild Muscle Mitochondrial Fusion Distress Extends Drosophila Lifespan through an Early and Systemic Metabolome Reorganization. Int J Mol Sci 2021; 22:ijms222212133. [PMID: 34830014 PMCID: PMC8618903 DOI: 10.3390/ijms222212133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
In a global aging population, it is important to understand the factors affecting systemic aging and lifespan. Mitohormesis, an adaptive response caused by different insults affecting the mitochondrial network, triggers a response from the nuclear genome inducing several pathways that promote longevity and metabolic health. Understanding the role of mitochondrial function during the aging process could help biomarker identification and the development of novel strategies for healthy aging. Herein, we interfered the muscle expression of the Drosophila genes Marf and Opa1, two genes that encode for proteins promoting mitochondrial fusion, orthologues of human MFN2 and OPA1. Silencing of Marf and Opa1 in muscle increases lifespan, improves locomotor capacities in the long term, and maintains muscular integrity. A metabolomic analysis revealed that muscle down-regulation of Marf and Opa1 promotes a non-autonomous systemic metabolome reorganization, mainly affecting metabolites involved in the energetic homeostasis: carbohydrates, lipids and aminoacids. Interestingly, the differences are consistently more evident in younger flies, implying that there may exist an anticipative adaptation mediating the protective changes at the older age. We demonstrate that mild mitochondrial muscle disturbance plays an important role in Drosophila fitness and reveals metabolic connections between tissues. This study opens new avenues to explore the link of mitochondrial dynamics and inter-organ communication, as well as their relationship with muscle-related pathologies, or in which muscle aging is a risk factor for their appearance. Our results suggest that early intervention in muscle may prevent sarcopenia and promote healthy aging.
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Affiliation(s)
- Andrea Tapia
- Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain; (A.T.); (M.P.-S.)
| | | | - Marta Roca
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain; (M.R.); (A.L.)
| | - Agustín Lahoz
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain; (M.R.); (A.L.)
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Antonio Pineda-Lucena
- Molecular Therapeutics Program, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona Spain;
| | - Víctor López del Amo
- Section of Cell and Developmental Biology, University of California, San Diego, CA 92093, USA
- Correspondence: (V.L.d.A.); (M.I.G.)
| | - Máximo Ibo Galindo
- Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain; (A.T.); (M.P.-S.)
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, 46022 Valencia, Spain
- UPV-CIPF Joint Unit Disease Mechanisms and Nanomedicine, 46012 Valencia, Spain
- Correspondence: (V.L.d.A.); (M.I.G.)
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16
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The Hitchhiker's Guide to Untargeted Lipidomics Analysis: Practical Guidelines. Metabolites 2021; 11:metabo11110713. [PMID: 34822371 PMCID: PMC8624948 DOI: 10.3390/metabo11110713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022] Open
Abstract
Lipidomics is a newly emerged discipline involving the identification and quantification of thousands of lipids. As a part of the omics field, lipidomics has shown rapid growth both in the number of studies and in the size of lipidome datasets, thus, requiring specific and efficient data analysis approaches. This paper aims to provide guidelines for analyzing and interpreting lipidome data obtained using untargeted methods that rely on liquid chromatography coupled with mass spectrometry (LC-MS) to detect and measure the intensities of lipid compounds. We present a state-of-the-art untargeted LC-MS workflow for lipidomics, from study design to annotation of lipid features, focusing on practical, rather than theoretical, approaches for data analysis, and we outline possible applications of untargeted lipidomics for biological studies. We provide a detailed R notebook designed specifically for untargeted lipidome LC-MS data analysis, which is based on xcms software.
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17
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Prieto J, García-Cañaveras JC, León M, Sendra R, Ponsoda X, Izpisúa Belmonte JC, Lahoz A, Torres J. c-MYC Triggers Lipid Remodelling During Early Somatic Cell Reprogramming to Pluripotency. Stem Cell Rev Rep 2021; 17:2245-2261. [PMID: 34476741 PMCID: PMC8599373 DOI: 10.1007/s12015-021-10239-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 11/30/2022]
Abstract
Metabolic rewiring and mitochondrial dynamics remodelling are hallmarks of cell reprogramming, but the roles of the reprogramming factors in these changes are not fully understood. Here we show that c-MYC induces biosynthesis of fatty acids and increases the rate of pentose phosphate pathway. Time-course profiling of fatty acids and complex lipids during cell reprogramming using lipidomics revealed a profound remodelling of the lipid content, as well as the saturation and length of their acyl chains, in a c-MYC-dependent manner. Pluripotent cells displayed abundant cardiolipins and scarce phosphatidylcholines, with a prevalence of monounsaturated acyl chains. Cells undergoing cell reprogramming showed an increase in mitochondrial membrane potential that paralleled that of mitochondrial-specific cardiolipins. We conclude that c-MYC controls the rewiring of somatic cell metabolism early in cell reprogramming by orchestrating cell proliferation, synthesis of macromolecular components and lipid remodelling, all necessary processes for a successful phenotypic transition to pluripotency.
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Affiliation(s)
- Javier Prieto
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain.,Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Marian León
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Ramón Sendra
- Departamento de Bioquímica y Biología Molecular, Universitat de València, 46100, Burjassot, Valencia, Spain
| | - Xavier Ponsoda
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain
| | | | - Agustín Lahoz
- Biomarkers and Precision Medicine Unit, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain.
| | - Josema Torres
- Departamento Biología Celular, Biología Funcional y Antropología Física, Universitat de València, 46100, Burjassot, Valencia, Spain. .,Instituto de Investigación Sanitaria (INCLIVA), 46010, Valencia, Spain.
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18
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Roca M, Alcoriza MI, Garcia-Cañaveras JC, Lahoz A. Reviewing the metabolome coverage provided by LC-MS: Focus on sample preparation and chromatography-A tutorial. Anal Chim Acta 2020; 1147:38-55. [PMID: 33485584 DOI: 10.1016/j.aca.2020.12.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Metabolomics has become an invaluable tool for both studying metabolism and biomarker discovery. The great technical advances in analytical chemistry and bioinformatics have considerably increased the number of measurable metabolites, yet an important part of the human metabolome remains uncovered. Among the various MS hyphenated techniques available, LC-MS stands out as the most used. Here, we aimed to show the capabilities of LC-MS to uncover part of the metabolome and how to best proceed with sample preparation and LC to maximise metabolite detection. The analyses of various open metabolite databases served us to estimate the size of the already detected human metabolome, the expected metabolite composition of most used human biospecimens and which part of the metabolome can be detected when LC-MS is used. Based on an extensive review and on our experience, we have outlined standard procedures for LC-MS analysis of urine, cells, serum/plasma, tissues and faeces, to guide in the selection of the sample preparation method that best matches with one or more LC techniques in order to get the widest metabolome coverage. These standard procedures may be a useful tool to explore, at a glance, the wide spectrum of possibilities available, which can be a good starting point for most of the LC-MS metabolomic studies.
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Affiliation(s)
- Marta Roca
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Maria Isabel Alcoriza
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Juan Carlos Garcia-Cañaveras
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Agustín Lahoz
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain; Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain.
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19
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Qiu J, Li T, Zhu ZJ. Multi-dimensional characterization and identification of sterols in untargeted LC-MS analysis using all ion fragmentation technology. Anal Chim Acta 2020; 1142:108-117. [PMID: 33280688 DOI: 10.1016/j.aca.2020.10.058] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022]
Abstract
Sterols are an important type of lipids, and play many important roles in physiological and pathological processes. However, comprehensive analysis of sterols especially identification of unknown sterols is challenging. In this work, LC-MS with all ion fragmentation (AIF) technology was developed for untargeted analysis of sterols in biological samples. AIF technology provided holistic and multi-dimensional characterization for both knowns and unknowns sterols, including accurate m/z, isotope pattern, retention time (RT), and co-eluted peak profiles between MS1 and MS2 ions in one analysis. We further developed an analysis strategy by integrating the multi-dimensional properties to support unambiguous identification of sterols, including distinguishing sterol isomers. The developed strategy enabled to identify a total of 23 sterols in mouse samples, and quantified 19 sterols in mouse liver tissues. More importantly, we demonstrated that AIF based multi-dimensional analysis provided a possibility to identify sterols without chemical standards and facilitated to discover novel compounds with sterol-like structures in biological samples. In summary, we employed the LC-MS based AIF technology to develop multi-dimensional characterization and identification of both known and unknown sterols in complex biological samples. The comprehensive analysis of sterols facilitates to provide molecular insights to many physiological and pathological activities in biology.
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Affiliation(s)
- Jiaqian Qiu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Tongzhou Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, PR China.
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20
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Sun T, Wang X, Cong P, Xu J, Xue C. Mass spectrometry-based lipidomics in food science and nutritional health: A comprehensive review. Compr Rev Food Sci Food Saf 2020; 19:2530-2558. [PMID: 33336980 DOI: 10.1111/1541-4337.12603] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/14/2020] [Accepted: 06/10/2020] [Indexed: 12/16/2022]
Abstract
With the advance in science and technology as well as the improvement of living standards, the function of food is no longer just to meet the needs of survival. Food science and its associated nutritional health issues have been increasingly debated. Lipids, as complex metabolites, play a key role both in food and human health. Taking advantages of mass spectrometry (MS) by combining its high sensitivity and accuracy with extensive selective determination of all lipid classes, MS-based lipidomics has been employed to resolve the conundrum of addressing both qualitative and quantitative aspects of high-abundance and low-abundance lipids in complex food matrices. In this review, we systematically summarize current applications of MS-based lipidomics in food field. First, common MS-based lipidomics procedures are described. Second, the applications of MS-based lipidomics in food science, including lipid composition characterization, adulteration, traceability, and other issues, are discussed. Third, the application of MS-based lipidomics for nutritional health covering the influence of food on health and disease is introduced. Finally, future research trends and challenges are proposed. MS-based lipidomics plays an important role in the field of food science, promoting continuous development of food science and integration of food knowledge with other disciplines. New methods of MS-based lipidomics have been developed to improve accuracy and sensitivity of lipid analysis in food samples. These developments offer the possibility to fully characterize lipids in food samples, identify novel functional lipids, and better understand the role of food in promoting healt.
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Affiliation(s)
- Tong Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xincen Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Peixu Cong
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jie Xu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Qingdao National Laboratory for Marine Science and Technology, Laboratory of Marine Drugs & Biological Products, Qingdao, China
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21
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Vieira NC, Cortelo PC, Castro-Gamboa I. Rapid qualitative profiling of metabolites present in Fusarium solani, a rhizospheric fungus derived from Senna spectabilis, using GC/MS and UPLC-QTOF/MS E techniques assisted by UNIFI information system. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2020; 26:281-291. [PMID: 32362135 DOI: 10.1177/1469066720922424] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fungi are an important source of natural products found in a variety of plant species. A wide range of methods for the detection of metabolites present in fungi have been reported in the literature. The search for methodologies that allow the rapid detection of compounds present in crude extracts is crucial to enable the metabolite annotation doing a qualitative analysis of the complex matrix. Mass spectrometry is an important ally when it comes to in silico detection of previously reported metabolites. In this work, the ethyl acetate extract of Fusarium solani was analyzed by gas chromatography coupled to mass spectrometry (GC/MS) after derivatization process. The ethyl acetate extract was also investigated by liquid chromatography coupled with high-resolution tandem mass spectrometry assisted by the UNIFI software system. A library containing previously reported metabolites from the Fusarium genus was added to the UNIFI platform. Simultaneously, the extract was analyzed through anticholinesterase and antifungal assays. The analysis of the derivatized extract by GC/MS led to the putative identification of five metabolites, and the investigation using Ultra-High Performance Liquid Chromatography - Quadrupole Time-of-Flight Mass Spectrometry (UPLC-QTOF) analysis in data-independent acquisition mode (mass spectrometry) led to the annotation of 15 compounds present in the built-in Fusarium library added to the UNIFI system. The Fusarium solani extract showed potential anticholinesterase and in vitro antifungal activity supported by the detection of bioactive metabolites.
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Affiliation(s)
- Natália Carolina Vieira
- Organic Chemistry Department, Institute of Chemistry, São Paulo State University (UNESP), São Paulo, Brazil
| | - Patrícia Cardoso Cortelo
- Organic Chemistry Department, Institute of Chemistry, São Paulo State University (UNESP), São Paulo, Brazil
| | - Ian Castro-Gamboa
- Organic Chemistry Department, Institute of Chemistry, São Paulo State University (UNESP), São Paulo, Brazil
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22
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Abstract
We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1-2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways.
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23
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Advances in Liquid Chromatography–Mass Spectrometry-Based Lipidomics: A Look Ahead. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00135-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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Tian H, Zhou Z, Shui G, Lam SM. Extensive Profiling of Polyphenols from two Trollius Species Using a Combination of Untargeted and Targeted Approaches. Metabolites 2020; 10:metabo10030119. [PMID: 32210165 PMCID: PMC7143900 DOI: 10.3390/metabo10030119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/13/2022] Open
Abstract
Various species of globeflowers, belonging to the genus Trollius, have been extensively used in traditional Chinese medicine due to their anti-inflammatory, antimicrobial, and antiviral properties, which are mainly attributed to their high polyphenol content. Differences in polyphenol composition, and abundances, will lead to varying treatment efficacies of globeflowers. Herein, we employ a combination of targeted and untargeted mass spectrometry (MS) approaches to characterize and quantify a comprehensive array of polyphenols, mainly including flavonoids and phenolic acids in two globeflower species commonly used in Chinese medicine, Trollius chinensis Bunge and Trollius ledebouri Reichb. In addition, free radical scavenging activity was investigated to evaluate the association between polyphenol composition and antioxidation capacity. Liquid chromatography (LC)-based separation and multiple-reaction-monitoring (MRM) transitions were optimized using a library of 78 polyphenol reference compounds to achieve absolute quantification on triple quadrupoles MS (QqQ). The analytical method was further expanded via high-resolution MS to provide relative quantitation of an additional 104 endogenous polyphenols in globeflowers not included in our reference library. Our results revealed stark differences in polyphenol content between T. chinensis and T. ledebouri, emphasizing the need for systematic characterization of polyphenol composition to ensure treatment efficacy and consistency in standardizing the use of globeflowers in Chinese medicine.
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Affiliation(s)
- He Tian
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhiyang Zhou
- Lipidall Technologies Company Limited, Changzhou 213022, China;
| | - Guanghou Shui
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- Correspondence: (G.S.); (S.M.L.); Tel.: +86-106-480-8831 (G.S.); +86-106-480-6670 (S.M.L.)
| | - Sin Man Lam
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- Lipidall Technologies Company Limited, Changzhou 213022, China;
- Correspondence: (G.S.); (S.M.L.); Tel.: +86-106-480-8831 (G.S.); +86-106-480-6670 (S.M.L.)
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25
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A new approach for characterization of phosphatidylcholines and lysophosphatidylcholine in human plasma. Bioanalysis 2020; 12:191-204. [PMID: 31983213 DOI: 10.4155/bio-2019-0280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: Characterization of phosphatidylcholines (PCs) and lysophosphatidylcholine in human plasma using LC-IT-MSn. The characterization approach was based on trapping the eluted positive ions and applying low voltage for fragmentation to MS2 and further fragmentation of the most abundant two peaks to obtain MS3. This approach allowed linking the MS3 data to MS2 and precursor ion. Methodology: The fatty acid part, at sn-1 and sn-2 of the glycerol backbone, could be identified based on the favored cleavage pathway. Conclusion: The dysregulated PCs and lysophosphatidylcholines in human plasma obtained from acute coronary syndrome cases, and Type 2 diabetes patients suffering no coronary syndromes were estimated and matched versus healthy volunteers. An epoxide form of 16:0-18:2 PC was confirmed, m/z 774.6.
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Lipidomics from sample preparation to data analysis: a primer. Anal Bioanal Chem 2019; 412:2191-2209. [PMID: 31820027 PMCID: PMC7118050 DOI: 10.1007/s00216-019-02241-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/09/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
Abstract
Lipids are amongst the most important organic compounds in living organisms, where they serve as building blocks for cellular membranes as well as energy storage and signaling molecules. Lipidomics is the science of the large-scale determination of individual lipid species, and the underlying analytical technology that is used to identify and quantify the lipidome is generally mass spectrometry (MS). This review article provides an overview of the crucial steps in MS-based lipidomics workflows, including sample preparation, either liquid–liquid or solid-phase extraction, derivatization, chromatography, ion-mobility spectrometry, MS, and data processing by various software packages. The associated concepts are discussed from a technical perspective as well as in terms of their application. Furthermore, this article sheds light on recent advances in the technology used in this field and its current limitations. Particular emphasis is placed on data quality assurance and adequate data reporting; some of the most common pitfalls in lipidomics are discussed, along with how to circumvent them.
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Stanstrup J, Broeckling CD, Helmus R, Hoffmann N, Mathé E, Naake T, Nicolotti L, Peters K, Rainer J, Salek RM, Schulze T, Schymanski EL, Stravs MA, Thévenot EA, Treutler H, Weber RJM, Willighagen E, Witting M, Neumann S. The metaRbolomics Toolbox in Bioconductor and beyond. Metabolites 2019; 9:E200. [PMID: 31548506 PMCID: PMC6835268 DOI: 10.3390/metabo9100200] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 11/17/2022] Open
Abstract
Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub.
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Affiliation(s)
- Jan Stanstrup
- Preventive and Clinical Nutrition, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark.
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO 80523, USA.
| | - Rick Helmus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany.
| | - Ewy Mathé
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA.
| | - Thomas Naake
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
| | - Luca Nicolotti
- The Australian Wine Research Institute, Metabolomics Australia, PO Box 197, Adelaide SA 5064, Australia.
| | - Kristian Peters
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Johannes Rainer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.
| | - Reza M Salek
- The International Agency for Research on Cancer, 150 cours Albert Thomas, CEDEX 08, 69372 Lyon, France.
| | - Tobias Schulze
- Department of Effect-Directed Analysis, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg.
| | - Michael A Stravs
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dubendorf, Switzerland.
| | - Etienne A Thévenot
- CEA, LIST, Laboratory for Data Sciences and Decision, MetaboHUB, Gif-Sur-Yvette F-91191, France.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
| | - Ralf J M Weber
- Phenome Centre Birmingham and School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands.
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, 85764 Neuherberg, Germany.
- Chair of Analytical Food Chemistry, Technische Universität München, 85354 Weihenstephan, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry (IPB Halle), Bioinformatics and Scientific Data, 06120 Halle, Germany.
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig Deutscher, Platz 5e, 04103 Leipzig, Germany.
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Yang Y, Deng J, Liu Y, He K, Xiang Z, Luan T. A microscale solid-phase microextraction probe for the in situ analysis of perfluoroalkyl substances and lipids in biological tissues using mass spectrometry. Analyst 2019; 144:5637-5645. [DOI: 10.1039/c9an01195a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An ambient mass spectrometry method for rapid, in situ, and microscale analysis of PFASs and lipids simultaneously in biological tissues for investigation of their biological correlation.
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Affiliation(s)
- Yunyun Yang
- Guangdong Engineering and Technology Research Center for Ambient Mass Spectrometry
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals
- Guangdong Institute of Analysis (China National Analytical Center Guangzhou)
- Guangzhou 510070
- China
| | - Jiewei Deng
- State Key Laboratory of Biocontrol
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center
- School of Life Sciences
- Sun Yat-Sen University
- Guangzhou 510275
| | - Yaohui Liu
- Guangdong Engineering and Technology Research Center for Ambient Mass Spectrometry
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals
- Guangdong Institute of Analysis (China National Analytical Center Guangzhou)
- Guangzhou 510070
- China
| | - Kaili He
- Guangdong Engineering and Technology Research Center for Ambient Mass Spectrometry
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals
- Guangdong Institute of Analysis (China National Analytical Center Guangzhou)
- Guangzhou 510070
- China
| | - Zhangmin Xiang
- Guangdong Engineering and Technology Research Center for Ambient Mass Spectrometry
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals
- Guangdong Institute of Analysis (China National Analytical Center Guangzhou)
- Guangzhou 510070
- China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol
- South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center
- School of Life Sciences
- Sun Yat-Sen University
- Guangzhou 510275
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