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Brunet TA, Clément Y, Calabrese V, Lemoine J, Geffard O, Chaumot A, Degli-Esposti D, Salvador A, Ayciriex S. Concomitant investigation of crustacean amphipods lipidome and metabolome during the molting cycle by Zeno SWATH data-independent acquisition coupled with electron activated dissociation and machine learning. Anal Chim Acta 2024; 1304:342533. [PMID: 38637034 DOI: 10.1016/j.aca.2024.342533] [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: 01/03/2024] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND DIA (Data-Independent Acquisition) is a powerful technique in Liquid Chromatography coupled with high-resolution tandem Mass Spectrometry (LC-MS/MS) initially developed for proteomics studies and recently emerging in metabolomics and lipidomics. It provides a comprehensive and unbiased coverage of molecules with improved reproducibility and quantitative accuracy compared to Data-Dependent Acquisition (DDA). Combined with the Zeno trap and Electron-Activated Dissociation (EAD), DIA enhances data quality and structural elucidation compared to conventional fragmentation under CID. These tools were applied to study the lipidome and metabolome of the freshwater amphipod Gammarus fossarum, successfully discriminating stages and highlighting significant biological features. Despite being underused, DIA, along with the Zeno trap and EAD, holds great potential for advancing research in the omics field. RESULTS DIA combined with the Zeno trap enhances detection reproducibility compared to conventional DDA, improving fragmentation spectra quality and putative identifications. LC coupled with Zeno-SWATH-DIA methods were used to characterize molecular changes in reproductive cycle of female gammarids. Multivariate data analysis including Principal Component Analysis and Partial Least Square Discriminant Analysis successfully identified significant features. EAD fragmentation helped to identify unknown features and to confirm their molecular structure using fragmentation spectra database annotation or machine learning. EAD database matching accurately annotated five glycerophospholipids, including the position of double bonds on fatty acid chain moieties. SIRIUS database predicted structures of unknown features based on experimental fragmentation spectra to compensate for database incompleteness. SIGNIFICANCE Reproducible detection of features and confident identification of putative compounds are pivotal stages within analytical pipelines. The DIA approach combined with Zeno pulsing enhances detection sensitivity and targeted fragmentation with EAD in positive polarity provides orthogonal fragmentation information. In our study, Zeno-DIA and EAD thereby facilitated a comprehensive and insightful exploration of pertinent biological molecules associated with the reproductive cycle of gammarids. The developed methodology holds great promises for identifying informative biomarkers on the health status of an environmental sentinel species.
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Affiliation(s)
- Thomas Alexandre Brunet
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Yohann Clément
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Valentina Calabrese
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Jérôme Lemoine
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Ecotoxicology Team, F-69625, Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Ecotoxicology Team, F-69625, Villeurbanne, France
| | | | - Arnaud Salvador
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France
| | - Sophie Ayciriex
- Univ Lyon, CNRS, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100, Villeurbanne, France.
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Pang Z, Xu L, Viau C, Lu Y, Salavati R, Basu N, Xia J. MetaboAnalystR 4.0: a unified LC-MS workflow for global metabolomics. Nat Commun 2024; 15:3675. [PMID: 38693118 PMCID: PMC11063062 DOI: 10.1038/s41467-024-48009-6] [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: 09/15/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024] Open
Abstract
The wide applications of liquid chromatography - mass spectrometry (LC-MS) in untargeted metabolomics demand an easy-to-use, comprehensive computational workflow to support efficient and reproducible data analysis. However, current tools were primarily developed to perform specific tasks in LC-MS based metabolomics data analysis. Here we introduce MetaboAnalystR 4.0 as a streamlined pipeline covering raw spectra processing, compound identification, statistical analysis, and functional interpretation. The key features of MetaboAnalystR 4.0 includes an auto-optimized feature detection and quantification algorithm for LC-MS1 spectra processing, efficient MS2 spectra deconvolution and compound identification for data-dependent or data-independent acquisition, and more accurate functional interpretation through integrated spectral annotation. Comprehensive validation studies using LC-MS1 and MS2 spectra obtained from standards mixtures, dilution series and clinical metabolomics samples have shown its excellent performance across a wide range of common tasks such as peak picking, spectral deconvolution, and compound identification with good computing efficiency. Together with its existing statistical analysis utilities, MetaboAnalystR 4.0 represents a significant step toward a unified, end-to-end workflow for LC-MS based global metabolomics in the open-source R environment.
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Affiliation(s)
- Zhiqiang Pang
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Lei Xu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Charles Viau
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Reza Salavati
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada.
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.
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Wu H, Yang L, Ren D, Gu Y, Ding X, Zhao Y, Fu G, Zhang H, Yi L. Combinatory data-independent acquisition and parallel reaction monitoring method for revealing the lipid metabolism biomarkers of coronary heart disease and its comorbidities. J Sep Sci 2024; 47:e2300848. [PMID: 38682821 DOI: 10.1002/jssc.202300848] [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: 11/16/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 05/01/2024]
Abstract
Disorders of lipid metabolism are a common cause of coronary heart disease (CHD) and its comorbidities. In this study, ultra-performance liquid chromatography-high-resolution mass spectrometry in data-independent acquisition (DIA) mode was applied to collect abundant tandem mass spectrometry data, which provided valuable information for lipid annotation. For the lipid isomers that could not be completely separated by chromatography, parallel reaction monitoring (PRM) mode was used for quantification. A total of 223 plasma lipid metabolites were annotated, and 116 of them were identified for their fatty acyl chain composition and location. In addition, 152 plasma lipids in patients with CHD and its comorbidities were quantitatively analyzed. Multivariate statistical analysis and metabolic pathway analysis demonstrated that glycerophospholipid and sphingolipid metabolism deserved more attention for CHD. This study proposed a method combining DIA and PRM for high-throughput characterization of plasma lipids. The results also improved our understanding of metabolic disorders of CHD and its comorbidities, which can provide valuable suggestions for medical intervention.
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Affiliation(s)
- Hao Wu
- Faculty of Chemical Engineering, Kunming University of Science and Technology, Kunming, China
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Lijuan Yang
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
| | - Dabing Ren
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
| | - Ying Gu
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
| | - Xiaoxue Ding
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- College of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yan Zhao
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- College of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Guanghui Fu
- School of Science, Kunming University of Science and Technology, Kunming, China
| | - Hong Zhang
- Department of Cardiology, First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- College of Medicine, Kunming University of Science and Technology, Kunming, China
| | - Lunzhao Yi
- Faculty of Chemical Engineering, Kunming University of Science and Technology, Kunming, China
- Faculty of Food Science and Engineering, Kunming University of Science and Technology, Kunming, China
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Xie Y, Liu X, Zhao C, Chen S, Wang S, Lin Z, Robison FM, George BM, Flynn RA, Lebrilla CB, Garcia BA. Development and application of GlycanDIA workflow for glycomic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584702. [PMID: 38559279 PMCID: PMC10980037 DOI: 10.1101/2024.03.12.584702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat on cells called the glycocalyx. The changes in glycosylation have been linked to the initiation and progression of many diseases. Thus, while the significance of glycosylation is well established, a lack of accessible methods to characterize glycans has hindered the ability to understand their biological functions. Mass spectrometry (MS)-based methods have generally been at the core of most glycan profiling efforts; however, modern data-independent acquisition (DIA), which could increase sensitivity and simplify workflows, has not been benchmarked for analyzing glycans. Herein, we developed a DIA-based glycomic workflow, termed GlycanDIA, to identify and quantify glycans with high sensitivity and accuracy. The GlycanDIA workflow combined higher energy collisional dissociation (HCD)-MS/MS and staggered windows for glycomic analysis, which facilitates the sensitivity in identification and the accuracy in quantification compared to conventional data-dependent acquisition (DDA)-based glycomics. To facilitate its use, we also developed a generic search engine, GlycanDIA Finder, incorporating an iterative decoy searching for confident glycan identification and quantification from DIA data. The results showed that GlycanDIA can distinguish glycan composition and isomers from N-glycans, O-glycans, and human milk oligosaccharides (HMOs), while it also reveals information on low-abundant modified glycans. With the improved sensitivity, we performed experiments to profile N-glycans from RNA samples, which have been underrepresented due to their low abundance. Using this integrative workflow to unravel the N-glycan profile in cellular and tissue glycoRNA samples, we found that RNA-glycans have specific forms as compared to protein-glycans and are also tissue-specific differences, suggesting distinct functions in biological processes. Overall, GlycanDIA can provide comprehensive information for glycan identification and quantification, enabling researchers to obtain in-depth and refined details on the biological roles of glycosylation.
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Affiliation(s)
- Yixuan Xie
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Xingyu Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Chenfeng Zhao
- Department of Computer Science & Engineering, Washington University, St. Louis, Missouri, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Shunyang Wang
- Department of Chemistry, University of California, Davis, Davis, California, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Faith M Robison
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Benson M George
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, United States
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, Davis, California, United States
- Department of Biochemistry, University of California, Davis, Davis, California, United States
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, United States
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Klont F, Nijdam FB, Bakker SJL, Keski-Rahkonen P, Hopfgartner G, Investigators T. High-abundance peaks and peak clusters associate with pharmaceutical polymers and excipients in urinary untargeted clinical metabolomics data: exploration of their origin and possible impact on label-free quantification. Analyst 2024; 149:1061-1067. [PMID: 38251754 PMCID: PMC10866140 DOI: 10.1039/d3an01874a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/08/2023] [Indexed: 01/23/2024]
Abstract
Pharmaceutical polymers and excipients represent interesting but often overlooked chemical classes in clinical exposure and bioanalytical research. These chemicals may cause hypersensitivity reactions, they can be useful to confirm exposure to pharmaceuticals, and they may pose bioanalytical challenges, including ion suppression in liquid chromatography-mass spectrometry (LC-MS-)based workflows. In this work, we assessed these chemicals in light of a rather surprising finding presented in two previously published studies, namely that usage of cyclosporine A, an immunosuppressive drug which is known to be cleared through excretion in the bile, explained the largest amount of variance in principal component analysis of urinary LC-SWATH/MS small-molecule profiling data. Specifically, we examined the freely-accessible 24-hour urine metabolomics data of 570 kidney transplant recipients included in the TransplantLines Biobank and Cohort Study (NCT03272841). These data unveiled thousands of high-abundance polymer peaks in some samples, which were associated with the use of the macrogol (i.e., polyethylene glycol) 3350 oral laxative agent. In addition, we found multiple clusters of high-abundance peaks which were linked to the exposure to two pharmaceutical excipients, namely short-chain polyethylene glycol (molecular weight <1000 Da) and polyethoxylated castor oil (also known as Kolliphor® EL or Cremophor® EL). Respectively, these excipients are used in temazepam capsules and cyclosporine A capsules, and the latter provides a plausible explanation for the rather surprising finding that instigated our work. Moreover, such explanation and our findings in general put emphasis on taking into consideration these and other pharmaceutical polymers and excipients when exploring, processing, and interpreting clinical small-molecule profiling data.
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Affiliation(s)
- Frank Klont
- Unit of PharmacoTherapy, -Epidemiology & -Economics, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211 Geneva, Switzerland
| | - Fleur B Nijdam
- Unit of PharmacoTherapy, -Epidemiology & -Economics, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands.
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands
| | - Pekka Keski-Rahkonen
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Avenue Tony Garnier 25, 69007 Lyon, France
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest Ansermet 24, 1211 Geneva, Switzerland
| | - TransplantLines Investigators
- Group of Authors on Behalf of the Transplant Lines Biobank and Cohort Study, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands
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6
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Ning J, Yang M, Liu W, Luo X, Yue X. Proteomics and Peptidomics As a Tool to Compare the Proteins and Endogenous Peptides in Human, Cow, and Donkey Milk. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:16435-16451. [PMID: 37882656 DOI: 10.1021/acs.jafc.3c04534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Cow's milk is the most widely used ingredient in infant formulas. However, its specific protein composition can cause allergic reactions. Finding alternatives to replace cow's milk and fill the nutritional gap with human milk is essential for the health of infants. Proteomic and peptidomic techniques have supported the elucidation of milk's nutritional ingredients. Recently, omics approaches have attracted increasing interest in the investigation of milk because of their high throughput, precision, sensitivity, and reproducibility. This review offers a significant overview of recent developments in proteomics and peptidomics used to study the differences in human, cow, and donkey milk. All three types of milks were identified to have critical biological functions in human health, particularly in infants. Donkey milk proteins were closer in composition to human milk, were less likely to cause allergic reactions, and may be developed as novel raw materials for formula milk powders.
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Affiliation(s)
- Jianting Ning
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Mei Yang
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Wanting Liu
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Xue Luo
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Xiqing Yue
- College of Food Science, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
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Chang JK, Teo G, Pewzner-Jung Y, Cuthbertson DJ, Futerman AH, Wenk MR, Choi H, Torta F. Q-RAI data-independent acquisition for lipidomic quantitative profiling. Sci Rep 2023; 13:19281. [PMID: 37935746 PMCID: PMC10630469 DOI: 10.1038/s41598-023-46312-8] [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: 01/31/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Untargeted lipidomics has been increasingly adopted for hypothesis generation in a biological context or discovery of disease biomarkers. Most of the current liquid chromatography mass spectrometry (LC-MS) based untargeted methodologies utilize a data dependent acquisition (DDA) approach in pooled samples for identification and MS-only acquisition for semi-quantification in individual samples. In this study, we present for the first time an untargeted lipidomic workflow that makes use of the newly implemented Quadrupole Resolved All-Ions (Q-RAI) acquisition function on the Agilent 6546 quadrupole time-of-flight (Q-TOF) mass spectrometer to acquire MS2 spectra in data independent acquisition (DIA) mode. This is followed by data processing and analysis on MetaboKit, a software enabling DDA-based spectral library construction and extraction of MS1 and MS2 peak areas, for reproducible identification and quantification of lipids in DIA analysis. This workflow was tested on lipid extracts from human plasma and showed quantification at MS1 and MS2 levels comparable to multiple reaction monitoring (MRM) targeted analysis of the same samples. Analysis of serum from Ceramide Synthase 2 (CerS2) null mice using the Q-RAI DIA workflow identified 88 lipid species significantly different between CerS2 null and wild type mice, including well-characterized changes previously associated with this phenotype. Our results show the Q-RAI DIA as a reliable option to perform simultaneous identification and reproducible relative quantification of lipids in exploratory biological studies.
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Affiliation(s)
- Jing Kai Chang
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Guoshou Teo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yael Pewzner-Jung
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Markus R Wenk
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Hyungwon Choi
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Federico Torta
- Precision Medicine Translational Research Programme and Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- SLING, Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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Li ZQ, Yin XL, Gu HW, Zou D, Ding B, Li Z, Chen Y, Long W, Fu H, She Y. Revealing the chemical differences and their application in the storage year prediction of Qingzhuan tea by SWATH-MS based metabolomics analysis. Food Res Int 2023; 173:113238. [PMID: 37803551 DOI: 10.1016/j.foodres.2023.113238] [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: 04/26/2023] [Revised: 06/19/2023] [Accepted: 06/27/2023] [Indexed: 10/08/2023]
Abstract
It's generally believed that the longer the storage, the better the quality of dark tea, but the chemical differences of Qingzhuan tea (QZT) with different storage years is still unclear. Herein, in this work, an untargeted metabolomic approach based on SWATH-MS was established to investigate the differential compounds of QZT with 0-9 years' storage time. These QZT samples were roughly divided into two categories by principal component analysis (PCA). After orthogonal projections to latent structures discriminant analysis (OPLS-DA), 18 differential compounds were putatively identified as chemical markers for the storage year variation of QZT. Heatmap visualization showed that the contents of catechins, fatty acids, and some phenolic acids significantly reduced, flavonoid glycosides, triterpenoids, and 8-C N-ethyl-2-pyrrolidinone-substituted flavan-3-ols (EPSFs) increased with the increase of storage time. Furthermore, these chemical markers were verified by the peak areas corresponding to MS2 ions from SWATH-MS. Based on the extraction chromatographic peak areas of MS and MS2 ions, a duration time prediction model was built for QZT with correlation coefficient R2 of 0.9080 and 0.9701, and RMSEP value of 0.85 and 1.24, respectively. This study reveals the chemical differences of QZT with different storage years and provides a theoretical basis for the quality evaluation of stored dark tea.
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Affiliation(s)
- Zhi-Quan Li
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Xiao-Li Yin
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China.
| | - Hui-Wen Gu
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Dan Zou
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Baomiao Ding
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Zhenshun Li
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Ying Chen
- College of Life Sciences, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou 434025, China
| | - Wanjun Long
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Haiyan Fu
- The Modernization Engineering Technology Research Center of Ethnic Minority Medicine of Hubei Province, School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China.
| | - Yuanbin She
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China.
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Saha S, Singh P, Dutta A, Vaidya H, Negi PC, Sengupta S, Seth S, Basak T. A Comprehensive Insight and Mechanistic Understanding of the Lipidomic Alterations Associated With DCM. JACC. ASIA 2023; 3:539-555. [PMID: 37614533 PMCID: PMC10442885 DOI: 10.1016/j.jacasi.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/17/2023] [Accepted: 06/03/2023] [Indexed: 08/25/2023]
Abstract
Dilated cardiomyopathy (DCM) is one of the major causes of heart failure characterized by the enlargement of the left ventricular cavity and contractile dysfunction of the myocardium. Lipids are the major sources of energy for the myocardium. Impairment of lipid homeostasis has a potential role in the pathogenesis of DCM. In this review, we have summarized the role of different lipids in the progression of DCM that can be considered as potential biomarkers. Further, we have also explained the mechanistic pathways followed by the lipid molecules in disease progression along with the cardioprotective role of certain lipids. As the global epidemiological status of DCM is alarming, it is high time to define some disease-specific biomarkers with greater prognostic value. We are proposing an adaptation of a system lipidomics-based approach to profile DCM patients in order to achieve a better diagnosis and prognosis of the disease.
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Affiliation(s)
- Shubham Saha
- School of Biosciences and Bioengineering. IIT-Mandi, Mandi, India
- BioX Center, Indian Institute of Technology-Mandi, Mandi, India
| | - Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Abhi Dutta
- School of Biosciences and Bioengineering. IIT-Mandi, Mandi, India
- BioX Center, Indian Institute of Technology-Mandi, Mandi, India
| | - Hiteshi Vaidya
- Department of Cardiology, Indira Gandhi Medical College & Hospital, Shimla, India
| | - Prakash Chand Negi
- Department of Cardiology, Indira Gandhi Medical College & Hospital, Shimla, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sandeep Seth
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, India
| | - Trayambak Basak
- School of Biosciences and Bioengineering. IIT-Mandi, Mandi, India
- BioX Center, Indian Institute of Technology-Mandi, Mandi, India
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Shi J, Wang Y, Liu Y, Xu Y. Analysis of Phospholipids in Digestion Using Hybrid IDA and SWATH Acquisition: An Example for Krill Oil. Foods 2023; 12:foods12102020. [PMID: 37238838 DOI: 10.3390/foods12102020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
The composition and digestion of phospholipid-rich foods have important effects on the health of the body. Herein, a model-assisted liquid chromatography coupling mass spectrometry (LC-MS) method was established to analyze the phosphatidylcholine (PC) and lyso-phosphatidylcholine (LPC) species in krill oil before and after digestion. According to the confirmed PC and LPC species in the IDA (information dependent acquisition) results, three categories of mathematical models were set up, involving the retention time (RT), carbon number and unsaturation degree of the fatty acyl chain. All of the regression coefficient values (R2) were greater than 0.90, showing satisfactory fitting results. On this basis, using the computationally created precursor ion mass of PC and LPC species, 12 extra PC species and 4 LPC species were found in the SWATH (sequential windowed acquisition of all theoretical fragment ions) results. The PC and LPC compositions in the final digestive products had obvious differences among the different krill oils with different phospholipid content. Furthermore, more than half of the LPC species in the final digestive products were newly generated, indicating that LPC was one of basic constituents in the digestive products of krill oil. In conclusion, model-assisted hybrid IDA and SWATH acquisition has excellent detection performance, contributing to deep studies of the formations and functions of phospholipids.
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Affiliation(s)
- Jiachen Shi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yanan Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
| | - Yongjiang Xu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, National Engineering Research Center for Functional Food, National Engineering Laboratory for Cereal Fermentation Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China
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11
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Theodoridis G, Gika H, Raftery D, Goodacre R, Plumb RS, Wilson ID. Ensuring Fact-Based Metabolite Identification in Liquid Chromatography-Mass Spectrometry-Based Metabolomics. Anal Chem 2023; 95:3909-3916. [PMID: 36791228 PMCID: PMC9979140 DOI: 10.1021/acs.analchem.2c05192] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Metabolite identification represents a major bottleneck in contemporary metabolomics research and a step where critical errors may occur and pass unnoticed. This is especially the case for studies employing liquid chromatography-mass spectrometry technology, where there is increased concern on the validity of the proposed identities. In the present perspective article, we describe the issue and categorize the errors into two types: identities that show poor biological plausibility and identities that do not comply with chromatographic data and thus to physicochemical properties (usually hydrophobicity/hydrophilicity) of the proposed molecule. We discuss the problem, present characteristic examples, and propose measures to improve the situation.
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Affiliation(s)
- Georgios Theodoridis
- Department
of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece,Biomic
AUTh, Center for Interdisciplinary Research
and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd., P.O. Box 8318, Thessaloniki 57001Greece,FoodOmicsGR,
AUTh node, Center for Interdisciplinary
Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, Thessaloniki 57001, Greece,
| | - Helen Gika
- Biomic
AUTh, Center for Interdisciplinary Research
and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd., P.O. Box 8318, Thessaloniki 57001Greece,FoodOmicsGR,
AUTh node, Center for Interdisciplinary
Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, Thessaloniki 57001, Greece,Laboratory
of Forensic Medicine and Toxicology, Department of Medicine, Aristotle University,
Thessaloniki 54124, Greece
| | - Daniel Raftery
- Northwest
Metabolomics Research Center, 850 Republican St., Seattle, Washington 98109, United States,Mitochondria
Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Royston Goodacre
- Centre
for Metabolomics Research, Department of Biochemistry and Systems
Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, United Kingdom
| | - Robert S. Plumb
- Scientific
Operations, IMMERSE, Waters Corporation, Cambridge 02142, Massachusetts United States
| | - Ian D. Wilson
- Centre
for Metabolomics Research, Department of Biochemistry and Systems
Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, United Kingdom,Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom,
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12
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Nutritional lipidomics for the characterization of lipids in food. ADVANCES IN FOOD AND NUTRITION RESEARCH 2023. [PMID: 37516469 DOI: 10.1016/bs.afnr.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lipids represent one out of three major macronutrient classes in the human diet. It is estimated to account for about 15-20% of the total dietary intake. Triacylglycerides comprise the majority of them, estimated 90-95%. Other lipid classes include free fatty acids, phospholipids, cholesterol, and plant sterols as minor components. Various methods are used for the characterization of nutritional lipids, however, lipidomics approaches become increasingly attractive for this purpose due to their wide coverage, comprehensiveness and holistic view on composition. In this chapter, analytical methodologies and workflows utilized for lipidomics profiling of food samples are outlined with focus on mass spectrometry-based assays. The chapter describes common lipid extraction protocols, the distinct instrumental mass-spectrometry based analytical platforms for data acquisition, chromatographic and ion-mobility spectrometry methods for lipid separation, briefly mentions alternative methods such as gas chromatography for fatty acid profiling and mass spectrometry imaging. Critical issues of important steps of lipidomics workflows such as structural annotation and identification, quantification and quality assurance are discussed as well. Applications reported over the period of the last 5years are summarized covering the discovery of new lipids in foodstuff, differential profiling approaches for comparing samples from different origin, species, varieties, cultivars and breeds, and for food processing quality control. Lipidomics as a powerful tool for personalized nutrition and nutritional intervention studies is briefly discussed as well. It is expected that this field is significantly growing in the near future and this chapter gives a short insight into the power of nutritional lipidomics approaches.
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13
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Tou K, Cawley A, Bowen C, Bishop DP, Fu S. Towards Non-Targeted Screening of Lipid Biomarkers for Improved Equine Anti-Doping. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010312. [PMID: 36615506 PMCID: PMC9822433 DOI: 10.3390/molecules28010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023]
Abstract
The current approach to equine anti-doping is focused on the targeted detection of prohibited substances. However, as new substances are rapidly being developed, the need for complimentary methods for monitoring is crucial to ensure the integrity of the racing industry is upheld. Lipidomics is a growing field involved in the characterisation of lipids, their function and metabolism in a biological system. Different lipids have various biological effects throughout the equine system including platelet aggregation and inflammation. A certain class of lipids that are being reviewed are the eicosanoids (inflammatory markers). The use of eicosanoids as a complementary method for monitoring has become increasingly popular with various studies completed to highlight their potential. Studies including various corticosteroids, non-steroidal anti-inflammatories and cannabidiol have been reviewed to highlight the progress lipidomics has had in contributing to the equine anti-doping industry. This review has explored the techniques used to prepare and analyse samples for lipidomic investigations in addition to the statistical analysis and potential for lipidomics to be used for a longitudinal assessment in the equine anti-doping industry.
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Affiliation(s)
- Kathy Tou
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW 2007, Australia
- Correspondence:
| | - Adam Cawley
- Australian Racing Forensic Laboratory, Racing NSW, Sydney, NSW 2000, Australia
| | - Christopher Bowen
- Mass Spectrometry Business Unit, Shimadzu Scientific Instruments (Australasia), Sydney, NSW 2116, Australia
| | - David P. Bishop
- Hyphenated Mass Spectrometry Laboratory (HyMAS), University of Technology, Sydney, NSW 2007, Australia
| | - Shanlin Fu
- Centre for Forensic Science, University of Technology Sydney, Sydney, NSW 2007, Australia
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14
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Peptidomics as a tool to analyze endogenous peptides in milk and milk-related peptides. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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15
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Xue G, Su S, Yan P, Shang J, Wang J, Yan C, Li J, Wang Q, Xiong X, Xu H. Integrative analyses of widely targeted metabolomic profiling and derivatization-based LC-MS/MS reveals metabolic changes of Zingiberis Rhizoma and its processed products. Food Chem 2022; 389:133068. [PMID: 35490521 DOI: 10.1016/j.foodchem.2022.133068] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/03/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Zingiberis Rhizoma (ZR) has nutritional value and application potentiality, while Zingiberis Rhizoma Praeparatum (ZRP) and Carbonised Ginger (CG) are two main processed products of ZR based on different methods. Here, we performed a widely targeted metabolomics method with Sequential Windowed Acquisition of all Theoretical fragment ions (SWATH) mode to analyze differential metabolites in ZR, ZRP and CG. Additionally, the chemical derivatization was applied to characterize different submetabolomes and improve the separation effect and MS response of metabolites. In total, 369 metabolites were identified and divided into 14 categories, 104 of which were differential metabolites. Our results suggest that carbohydrates, nucleotides, organic acids, vitamins, lipids, indoles, alkaloids, and terpenes contributed to a downward trend after processing, but the maximum content of flavanones, phenylpropanes and polyphenols appeared in ZRP, and that of alcohols appeared in CG. These findings serve as promising perspectives for developing functional food in ZR, ZRP and CG.
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Affiliation(s)
- Guiren Xue
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Shanshan Su
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Pengfei Yan
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Jiawei Shang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Jianxin Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Chengye Yan
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Jiaxi Li
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Qiao Wang
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Xue Xiong
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China
| | - Huijun Xu
- Department of Pharmaceutical Analysis, School of Pharmacy, Hebei Medical University, Shijiazhuang 050017, PR China.
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16
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A Novel Approach of SWATH-Based Metabolomics Analysis Using the Human Metabolome Database Spectral Library. Int J Mol Sci 2022; 23:ijms231810908. [PMID: 36142821 PMCID: PMC9500730 DOI: 10.3390/ijms231810908] [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: 08/18/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/22/2022] Open
Abstract
Metabolomics is a potential approach to paving new avenues for clinical diagnosis, molecular medicine, and therapeutic drug monitoring and development. The conventional metabolomics analysis pipeline depends on the data-independent acquisition (DIA) technique. Although powerful, it still suffers from stochastic, non-reproducible ion selection across samples. Despite the presence of different metabolomics workbenches, metabolite identification remains a tedious and time-consuming task. Consequently, sequential windowed acquisition of all theoretical MS (SWATH) acquisition has attracted much attention to overcome this limitation. This article aims to develop a novel SWATH platform for data analysis with a generation of an accurate mass spectral library for metabolite identification using SWATH acquisition. The workflow was validated using inclusion/exclusion compound lists. The false-positive identification was 3.4% from the non-endogenous drugs with 96.6% specificity. The workflow has proven to overcome background noise despite the complexity of the SWATH sample. From the Human Metabolome Database (HMDB), 1282 compounds were tested in various biological samples to demonstrate the feasibility of the workflow. The current study identified 377 compounds in positive and 303 in negative modes with 392 unique non-redundant metabolites. Finally, a free software tool, SASA, was developed to analyze SWATH-acquired samples using the proposed pipeline.
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17
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Lipidomics: An excellent tool for chronic disease detection. Curr Res Transl Med 2022; 70:103346. [PMID: 35487168 DOI: 10.1016/j.retram.2022.103346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 03/10/2022] [Accepted: 04/04/2022] [Indexed: 01/31/2023]
Abstract
It has been known as almost all the cells consists a lipid molecule which has a considerable impact in various biological processes. Lipids have been investigated with a potential role for the formation of cellular membrane and thereby maintaining the structural integrity. Omics has placed as a combined technologies utilized for an exploaration of mechanistic actions in several kinds of molecules that make up the cells of an organism. Lipidomics has been recognized as a newly emerged branch of omics technology. This technology has the captivating factors to classify and characterize almost all the cellular lipids with the help of various analytical techniques and computational biological plateform. In lipidomics studies, structural display of several lipid biomarkers could also be analyzed and considered for actual disease diagnosis procedures. This could also replace certain traditional diagnostics method at all over the globe. Our review focuses how important this lipidomics particularly in disease diagnosis and also covers various analytical techniques and computational methods or bioinformatics tools in for the diagnosis of disease. In addtion, we also pinponted the possible role of lipids in several kinds of cellular disorders including cancer, neurodegenerative diseases, cardiovascular diseases, diabetes and obesity in human population. .
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18
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Duan L, Scheidemantle G, Lodge M, Cummings MJ, Pham E, Wang X, Kennedy A, Liu X. Prioritize biologically relevant ions for data-independent acquisition (BRI-DIA) in LC-MS/MS-based lipidomics analysis. Metabolomics 2022; 18:55. [PMID: 35842862 DOI: 10.1007/s11306-022-01913-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/27/2022] [Indexed: 10/17/2022]
Abstract
INTRODUCTION Data-dependent acquisition (DDA) is the most commonly used MS/MS scan method for lipidomics analysis on orbitrap-based instrument. However, MS instrument associated software decide the top N precursors for fragmentation, resulting in stochasticity of precursor selection and compromised consistency and reproducibility. We introduce a novel workflow using biologically relevant lipids to construct inclusion list for data-independent acquisition (DIA), named as BRI-DIA workflow. OBJECTIVES To ensure consistent coverage of biologically relevant lipids in LC-MS/MS-based lipidomics analysis. METHODS Biologically relevant ion list was constructed based on LIPID MAPS and lipidome atlas in MS-DIAL 4. Lipids were extracted from mouse tissues and used to assess different MS/MS scan workflow (DDA, BRI-DIA, and hybrid mode) on LC-Orbitrap Exploris 480 mass spectrometer. RESULTS DDA resulted in more MS/MS events, but the total number of unique lipids identified by three methods (DDA, BRI-DIA, and hybrid MS/MS scan mode) is comparable (580 unique lipids across 44 lipid subclasses in mouse liver). Major cardiolipin molecular species were identified by data generated using BRI-DIA and hybrid methods and allowed calculation of cardiolipin compositions, while identification of the most abundant cardiolipin CL72:8 was missing in data generated using DDA method, leading to wrong calculation of cardiolipin composition. CONCLUSION The method of using inclusion list comprised of biologically relevant lipids in DIA MS/MS scan is as efficient as traditional DDA method in profiling lipids, but offers better consistency of lipid identification, compared to DDA method. This study was performed using Orbitrap Exploris 480, and we will further evaluate this workflow on other platforms, and if verified by future work, this biologically relevant ion fragmentation workflow could be routinely used in many studies to improve MS/MS identification capacities.
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Affiliation(s)
- Likun Duan
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Grace Scheidemantle
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Mareca Lodge
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Magdalina J Cummings
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27695, USA
| | - Eva Pham
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xiaoqiu Wang
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
- The Comparative Medicine Institute, North Carolina State University, Raleigh, NC, 27695, USA
| | - Arion Kennedy
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xiaojing Liu
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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19
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Shi J, Wang T, Guo H, Li C, Li L, Jin Y, Chen H, Huang J. High-resolution mass spectrometry assay for quantifying ceramides and dihydroceramides in the cerebrospinal fluid from patients who experienced intracranial infection after craniotomy. J Pharm Biomed Anal 2022; 219:114907. [PMID: 35772235 DOI: 10.1016/j.jpba.2022.114907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
Ceramides (CERs) and dihydroceramides (dhCERs) are biologically active lipids involved in cell proliferation, differentiation, and apoptosis, as well as associated with infectious diseases. The concentration of CERs and dhCERs in the cerebrospinal fluid (CSF) could potentially allow the distinction of patients with intracranial infection (ICI) after craniotomy from controls, but the quantification is limited by their ultralow concentrations. Therefore, a novel high performance liquid chromatography-triple-quadrupole/time-of-flight mass spectrometry (HPLC-QTOF-MS) with Sequential Window Acquisition of All Theoretical Fragment Ion Spectra (SWATH) was applied to measure CERs and dhCERs in CSF, since it possesses a higher sensitivity (LLOQ = 0.1 pmol/mL) than the multiple reaction monitoring (MRM) acquisition carried on triple quadrupole (QqQ) MS. This method was validated and applied to CSF samples from patients who experienced postoperative ICI (63 patients) and controls who did not experience it after surgery (62 patients). This assay was linear over the measuring range 0.1-100 pmol/mL for these CER and dhCER species with good accuracy and precision. Elevated CERs and dhCERs were observed in CSF from patients who experienced postoperative ICI. CER 16:0 was found with a clinical sensitivity of 93.65 % and specificity of 87.1 % in distinguishing the 63 patients with ICI from the 62 controls. Therefore, this method could be applied in the detection of CERs and dhCERs in CSF, which were correlated with the presence of ICI.
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Affiliation(s)
- Jiawei Shi
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin 130021, China
| | - Tingting Wang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin 130021, China
| | - Haiyang Guo
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin 130021, China
| | - Chen Li
- Department of Neurosurgery, The First Hospital of Jilin University, Jilin 130021, China
| | - Li Li
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin 130021, China
| | - Yuting Jin
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin 130021, China
| | - Haizhen Chen
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin 130021, China
| | - Jing Huang
- Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin 130021, China; Department of Neurosurgery, The First Hospital of Jilin University, Jilin 130021, China.
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20
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Santacruz CA, Vincent JL, Duitama J, Bautista E, Imbault V, Bruneau M, Creteur J, Brimioulle S, Communi D, Taccone FS. The Cerebrospinal Fluid Proteomic Response to Traumatic and Nontraumatic Acute Brain Injury: A Prospective Study. Neurocrit Care 2022; 37:463-470. [PMID: 35523916 DOI: 10.1007/s12028-022-01507-1] [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: 10/29/2021] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Quantitative analysis of ventricular cerebrospinal fluid (vCSF) proteins following acute brain injury (ABI) may help identify pathophysiological pathways and potential biomarkers that can predict unfavorable outcome. METHODS In this prospective proteomic analysis study, consecutive patients with severe ABI expected to require intraventricular catheterization for intracranial pressure (ICP) monitoring for at least 5 days and patients without ABI admitted for elective clipping of an unruptured cerebral aneurysm were included. vCSF samples were collected within the first 24 h after ABI and ventriculostomy insertion and then every 24 h for 5 days. In patients without ABI, a single vCSF sample was collected at the time of elective clipping. Data-independent acquisition and sequential window acquisition of all theoretical spectra (SWATH) mass spectrometry were used to compare differences in protein expression in patients with ABI and patients without ABI and in patients with traumatic and nontraumatic ABI. Differences in protein expression according to different ICP values, intensive care unit outcome, subarachnoid hemorrhage (SAH) versus traumatic brain injury (TBI), and good versus poor 3-month functional status (assessed by using the Glasgow Outcome Scale) were also evaluated. vCSF proteins with significant differences between groups were compared by using linear models and selected for gene ontology analysis using R Language and the Panther database. RESULTS We included 50 patients with ABI (SAH n = 23, TBI n = 15, intracranial hemorrhage n = 6, ischemic stroke n = 3, others n = 3) and 12 patients without ABI. There were significant differences in the expression of 255 proteins between patients with and without ABI (p < 0.01). There were intraday and interday differences in expression of seven proteins related to increased inflammation, apoptosis, oxidative stress, and cellular response to hypoxia and injury. Among these, glial fibrillary acidic protein expression was higher in patients with ABI with severe intracranial hypertension (ICH) (ICP ≥ 30 mm Hg) or death compared to those without (log 2 fold change: + 2.4; p < 0.001), suggesting extensive primary astroglial injury or death. There were differences in the expression of 96 proteins between patients with traumatic and nontraumatic ABI (p < 0.05); intraday and interday differences were observed for six proteins related to structural damage, complement activation, and cholesterol metabolism. Thirty-nine vCSF proteins were associated with an increased risk of severe ICH (ICP ≥ 30 mm Hg) in patients with traumatic compared with nontraumatic ABI (p < 0.05). No significant differences were found in protein expression between patients with SAH versus TBI or between those with good versus poor 3-month Glasgow Outcome Scale score. CONCLUSIONS Dysregulated vCSF protein expression after ABI may be associated with an increased risk of severe ICH and death.
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Affiliation(s)
- Carlos A Santacruz
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
- Department of Intensive and Critical Care Medicine, Academic Hospital Fundación Santa Fe de Bogota Foundation, Bogota, Colombia
| | - Jean-Louis Vincent
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogota, Colombia
| | - Edwin Bautista
- Systems and Computing Engineering Department, Universidad de los Andes, Bogota, Colombia
| | - Virginie Imbault
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Michaël Bruneau
- Department of Neurosurgery, Erasme Hospital, Université Libre de Bruxelles, Route De Lennik 808, 1070, Brussels, Belgium
| | - Jacques Creteur
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Serge Brimioulle
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - David Communi
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Fabio S Taccone
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
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21
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Comprehensive profiling of conjugated fatty acid isomers and their lipid oxidation products by two-dimensional chiral RP×RP liquid chromatography hyphenated to UV- and SWATH-MS-detection. Anal Chim Acta 2022; 1202:339667. [DOI: 10.1016/j.aca.2022.339667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 11/23/2022]
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22
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Schoeny H, Rampler E, Binh Chu D, Schoeberl A, Galvez L, Blaukopf M, Kosma P, Koellensperger G. Achieving Absolute Molar Lipid Concentrations: A Phospholipidomics Cross-Validation Study. Anal Chem 2022; 94:1618-1625. [PMID: 35025205 PMCID: PMC8792901 DOI: 10.1021/acs.analchem.1c03743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/05/2022] [Indexed: 01/28/2023]
Abstract
Standardization is essential in lipidomics and part of a huge community effort. However, with the still ongoing lack of reference materials, benchmarking quantification is hampered. Here, we propose traceable lipid class quantification as an important layer for the validation of quantitative lipidomics workflows. 31P nuclear magnetic resonance (NMR) and inductively coupled plasma (ICP)-mass spectrometry (MS) can use certified species-unspecific standards to validate shotgun or liquid chromatography (LC)-MS-based lipidomics approaches. We further introduce a novel lipid class quantification strategy based on lipid class separation and mass spectrometry using an all ion fragmentation (AIF) approach. Class-specific fragments, measured over a mass range typical for the lipid classes, are integrated to assess the lipid class concentration. The concept proved particularly interesting as low absolute limits of detection in the fmol range were achieved and LC-MS platforms are widely used in the field of lipidomics, while the accessibility of NMR and ICP-MS is limited. Using completely independent calibration strategies, the introduced validation scheme comprised the quantitative assessment of the complete phospholipid sub-ome, next to the individual lipid classes. Komagataella phaffii served as a prime example, showcasing mass balances and supporting the value of benchmarks for quantification at the lipid species level.
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Affiliation(s)
- Harald Schoeny
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Evelyn Rampler
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- Vienna
Metabolomics Center (VIME), University of
Vienna, Althanstraße
14, 1090 Vienna, Austria
- Chemistry
Meets Microbiology, Althanstraße
14, 1090 Vienna, Austria
| | - Dinh Binh Chu
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- School
of Chemical Engineering, Hanoi University
of Science and Technology, 1 Dai Co Viet, Hai Ba Trung, Hanoi 100000, Vietnam
| | - Anna Schoeberl
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Luis Galvez
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
| | - Markus Blaukopf
- Department
of Chemistry, University of Natural Resources
and Life Sciences Vienna, 1190 Vienna, Austria
| | - Paul Kosma
- Department
of Chemistry, University of Natural Resources
and Life Sciences Vienna, 1190 Vienna, Austria
| | - Gunda Koellensperger
- Department
of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090 Vienna, Austria
- Vienna
Metabolomics Center (VIME), University of
Vienna, Althanstraße
14, 1090 Vienna, Austria
- Chemistry
Meets Microbiology, Althanstraße
14, 1090 Vienna, Austria
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23
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Castelli FA, Rosati G, Moguet C, Fuentes C, Marrugo-Ramírez J, Lefebvre T, Volland H, Merkoçi A, Simon S, Fenaille F, Junot C. Metabolomics for personalized medicine: the input of analytical chemistry from biomarker discovery to point-of-care tests. Anal Bioanal Chem 2022; 414:759-789. [PMID: 34432105 PMCID: PMC8386160 DOI: 10.1007/s00216-021-03586-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/30/2022]
Abstract
Metabolomics refers to the large-scale detection, quantification, and analysis of small molecules (metabolites) in biological media. Although metabolomics, alone or combined with other omics data, has already demonstrated its relevance for patient stratification in the frame of research projects and clinical studies, much remains to be done to move this approach to the clinical practice. This is especially true in the perspective of being applied to personalized/precision medicine, which aims at stratifying patients according to their risk of developing diseases, and tailoring medical treatments of patients according to individual characteristics in order to improve their efficacy and limit their toxicity. In this review article, we discuss the main challenges linked to analytical chemistry that need to be addressed to foster the implementation of metabolomics in the clinics and the use of the data produced by this approach in personalized medicine. First of all, there are already well-known issues related to untargeted metabolomics workflows at the levels of data production (lack of standardization), metabolite identification (small proportion of annotated features and identified metabolites), and data processing (from automatic detection of features to multi-omic data integration) that hamper the inter-operability and reusability of metabolomics data. Furthermore, the outputs of metabolomics workflows are complex molecular signatures of few tens of metabolites, often with small abundance variations, and obtained with expensive laboratory equipment. It is thus necessary to simplify these molecular signatures so that they can be produced and used in the field. This last point, which is still poorly addressed by the metabolomics community, may be crucial in a near future with the increased availability of molecular signatures of medical relevance and the increased societal demand for participatory medicine.
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Affiliation(s)
- Florence Anne Castelli
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Giulio Rosati
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Christian Moguet
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Celia Fuentes
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jose Marrugo-Ramírez
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Thibaud Lefebvre
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- Centre de Recherche sur l'Inflammation/CRI, Université de Paris, Inserm, Paris, France
- CRMR Porphyrie, Hôpital Louis Mourier, AP-HP Nord - Université de Paris, Colombes, France
| | - Hervé Volland
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - Arben Merkoçi
- Institut Català de Nanociència i Nanotecnologia (ICN2), Edifici ICN2 Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Stéphanie Simon
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
| | - François Fenaille
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France
- MetaboHUB, Gif-sur-Yvette, France
| | - Christophe Junot
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (MTS), Gif-sur-Yvette cedex, 91191, France.
- MetaboHUB, Gif-sur-Yvette, France.
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24
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Tian Z, Liu F, Li D, Fernie AR, Chen W. Strategies for structure elucidation of small molecules based on LC–MS/MS data from complex biological samples. Comput Struct Biotechnol J 2022; 20:5085-5097. [PMID: 36187931 PMCID: PMC9489805 DOI: 10.1016/j.csbj.2022.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/03/2022] [Accepted: 09/03/2022] [Indexed: 11/06/2022] Open
Abstract
LC–MS/MS is a major analytical platform for metabolomics, which has become a recent hotspot in the research fields of life and environmental sciences. By contrast, structure elucidation of small molecules based on LC–MS/MS data remains a major challenge in the chemical and biological interpretation of untargeted metabolomics datasets. In recent years, several strategies for structure elucidation using LC–MS/MS data from complex biological samples have been proposed, these strategies can be simply categorized into two types, one based on structure annotation of mass spectra and for the other on retention time prediction. These strategies have helped many scientists conduct research in metabolite-related fields and are indispensable for the development of future tools. Here, we summarized the characteristics of the current tools and strategies for structure elucidation of small molecules based on LC–MS/MS data, and further discussed the directions and perspectives to improve the power of the tools or strategies for structure elucidation.
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25
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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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26
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Li L, Wang Y, Li Y, Zhu H, Feng B. A pseudotargeted method based on sequential window acquisition of all theoretical spectra mass spectrometry acquisition and its application in quality assessment of traditional Chinese medicine preparation-Yuanhu Zhitong tablet. J Sep Sci 2021; 45:650-658. [PMID: 34794207 DOI: 10.1002/jssc.202100611] [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: 08/03/2021] [Revised: 11/08/2021] [Accepted: 11/13/2021] [Indexed: 11/07/2022]
Abstract
Quality control plays a key role in the application of Chinese materia medica, especially in the preparation of traditional Chinese medicine. A pseudotargeted analysis method using an ultra-high-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry that was operated in the sequential window acquisition of all theoretical spectra mode was proposed to explore the chemical markers of traditional Chinese medicine preparation. Full-scan-based untargeted analysis was applied to extract the target ions. After data preprocessing, 302 target ions were extracted and used for the subsequent sequential window acquisition of all theoretical spectra analyses. The established sequential window acquisition of all theoretical spectra-based pseudotargeted approaches exhibited good repeatability and a wide linear range. The established method was successfully applied to discover analytical markers for the Yuanhu Zhitong tablet. After multivariate statistical analysis, 94 potential markers were identified. Ten markers were annotated by matching accurate m/z and product ion information obtained from previous reports. It is clearly indicated that the pseudotargeted analysis could make a great contribution to the quality assessment of traditional Chinese medicine preparation as a newly emerging technique.
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Affiliation(s)
- Lele Li
- School of Pharmacy, Jilin Medical University, Jilin, P. R. China
| | - Yang Wang
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, P. R. China
| | - Yuxuan Li
- School of Pharmacy, Jilin Medical University, Jilin, P. R. China
| | - Heyun Zhu
- School of Pharmacy, Jilin Medical University, Jilin, P. R. China
| | - Bo Feng
- School of Pharmacy, Jilin Medical University, Jilin, P. R. China
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27
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Matsuzawa Y, Higashi Y, Takano K, Takahashi M, Yamada Y, Okazaki Y, Nakabayashi R, Saito K, Tsugawa H. Food Lipidomics for 155 Agricultural Plant Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8981-8990. [PMID: 33570932 DOI: 10.1021/acs.jafc.0c07356] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lipids exhibit functional bioactivities based on their polar and acyl chain properties; humans obtain lipids from dietary plant product intake. Therefore, the identification of different molecular species facilitates the evaluation of biological functions and nutrition levels and new phenotype-modulating lipid structures. As a rapid screening strategy, we performed untargeted lipidomics for 155 agricultural products in 58 species from 23 plant families, wherein product-specific lipid diversities were shown using computational mass spectrometry. We characterized 716 lipid species, for which the profiles revealed the National Center for Biotechnology Information-established organismal classification and unique plant tissue metabotypes. Moreover, we annotated unreported subclasses in plant lipidology; e.g., triacylglycerol estolide (TG-EST) was detected in rice seeds (Oryza sativa) and several plant species. TG-EST is known as the precursor molecule producing the fatty acid ester of hydroxy fatty acid, which lowers ambient glycemia and improves glucose tolerance. Hence, our method can identify agricultural plant products containing valuable lipid ingredients.
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Affiliation(s)
- Yuki Matsuzawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Yasuhiro Higashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kouji Takano
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikiko Takahashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yutaka Yamada
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507 Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
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28
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Shanthamoorthy P, Young A, Röst H. Analyzing Assay Specificity in Metabolomics Using Unique Ion Signature Simulations. Anal Chem 2021; 93:11415-11423. [PMID: 34375078 DOI: 10.1021/acs.analchem.1c01204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeted, untargeted, and data-independent acquisition (DIA) metabolomics workflows are often hampered by ambiguous identification based on either MS1 information alone or relatively few MS2 fragment ions. While DIA methods have been popularized in proteomics, it is less clear whether they are suitable for metabolomics workflows due to their large precursor isolation windows and complex coisolation patterns. Here, we quantitatively investigate the conditions necessary for unique metabolite detection in complex backgrounds using precursor and fragment ion mass-to-charge (m/z) separation, comparing three benchmarked mass spectrometry (MS) methods [MS1, MRM (multiple reaction monitoring), and DIA]. Our simulations show that DIA outperformed MS1-only and MRM-based methods with regards to specificity by factors of ∼2.8-fold and ∼1.8-fold, respectively. Additionally, we show that our results are not dependent on the number of transitions used or the complexity of the background matrix. Finally, we show that collision energy is an important factor in unambiguous detection and that a single collision energy setting per compound cannot achieve optimal pairwise differentiation of compounds. Our analysis demonstrates the power of using both high-resolution precursor and high-resolution fragment ion m/z for unambiguous compound detection. This work also establishes DIA as an emerging MS acquisition method with high selectivity for metabolomics, outperforming both data-dependent acquisition (DDA) and MRM with regards to unique compound identification potential.
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Affiliation(s)
- Premy Shanthamoorthy
- Terrence Donnelly Centre for Cellular Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Adamo Young
- Terrence Donnelly Centre for Cellular Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Hannes Röst
- Terrence Donnelly Centre for Cellular Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
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29
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Shen H, Zhang Y, Schramm KW. Analytical aspects of meet-in-metabolite analysis for molecular pathway reconstitution from exposure to adverse outcome. Mol Aspects Med 2021; 87:101006. [PMID: 34304900 DOI: 10.1016/j.mam.2021.101006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 06/05/2021] [Accepted: 07/20/2021] [Indexed: 12/22/2022]
Abstract
To explore the etiology of diseases is one of the major goals in epidemiological study. Meet-in-metabolite analysis reconstitutes biomonitoring-based adverse outcome (AO) pathways from environmental exposure to a disease, in which the chemical exposome-related metabolism responses are transmitted to incur the AO-related metabolism phenotypes. However, the ongoing data-dependent acquisition of non-targeted biomonitoring by high-resolution mass spectrometry (HRMS) is biased against the low abundance molecules, which forms the major of molecular internal exposome, i.e., the totality of trace levels of environmental pollutants and/or their metabolites in human samples. The recent development of data-independent acquisition protocols for HRMS screening has opened new opportunities to enhance unbiased measurement of the extremely low abundance molecules, which can encompass a wide range of analytes and has been applied in metabolomics, DNA, and protein adductomics. In addition, computational MS for small molecules is urgently required for the top-down exposome databases. Although a holistic analysis of the exposome and endogenous metabolites is plausible, multiple and flexible strategies, instead of "putting one thing above all" are proposed.
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Affiliation(s)
- Heqing Shen
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, PR China.
| | - Yike Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, 361102, Xiamen, PR China
| | - Karl-Werner Schramm
- Helmholtz Zentrum München, Molecular EXposomics, German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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30
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Hyötyläinen T. Analytical challenges in human exposome analysis with focus on environmental analysis combined with metabolomics. J Sep Sci 2021; 44:1769-1787. [PMID: 33650238 DOI: 10.1002/jssc.202001263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Environmental factors, such as chemical exposures, are likely to play a crucial role in the development of several human chronic diseases. However, how the specific exposures contribute to the onset and progress of various diseases is still poorly understood. In part, this is because comprehensive characterization of the chemical exposome is a highly challenging task, both due to its complex dynamic nature as well as due to the analytical challenges. Herein, the analytical challenges in the field of exposome research are reviewed, with specific emphasis on the sampling, sample preparation, and analysis, as well as challenges in the compound identification. The primary focus is on the human chemical exposome, that is, exposures to mixtures of environmental chemicals and its impact on human metabolome. In order to highlight the recent progress in the exposome research in relation to human health and disease, selected examples of human exposome studies are presented.
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Affiliation(s)
- Tuulia Hyötyläinen
- MTM Research Centre, School of Science and Technology, Örebro University, Örebro, Sweden
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31
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Mehl A, Schmidt LJ, Schmidt L, Morlock GE. High-throughput planar solid-phase extraction coupled to orbitrap high-resolution mass spectrometry via the autoTLC-MS interface for screening of 66 multi-class antibiotic residues in food of animal origin. Food Chem 2021; 351:129211. [PMID: 33636534 DOI: 10.1016/j.foodchem.2021.129211] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/14/2020] [Accepted: 01/23/2021] [Indexed: 02/07/2023]
Abstract
Antibiotic residues in food pose a major threat to the health of humans and animals worldwide. Their trace-level analysis is still too time- and cost-intensive to be adequately covered in routine analysis. Thus, a new high-throughput planar solid-phase extraction method has been developed for rapid screening of 66 antibiotics. Via simple clicks on the image, the autoTLC-MS interface automatically eluted the target analyte zones directly into an orbitrap high-resolution mass spectrometer operated in the variable data-independent acquisition mode. Muscle tissue, cow milk and chicken eggs were analyzed regarding nine different antibiotic classes, including sulfonamides, diaminopyrimidines, lincosamides, pleuromutilins, macrolides, cephalosporins, penicillins, amphenicols and nitroimidazoles. The planar clean-up took 7 min per sample, which is 5-fold faster than the routine state-of-the-art. The screening method has been validated for one representative of each class according to the European Commission Decision 2002/657/EC. Most analytes were successfully detected at half of their required maximum residue limit.
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Affiliation(s)
- Annabel Mehl
- Chair of Food Science, Institute of Nutritional Science, and Interdisciplinary Research Center, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Lena J Schmidt
- Chair of Food Science, Institute of Nutritional Science, and Interdisciplinary Research Center, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Laszlo Schmidt
- Chair of Food Science, Institute of Nutritional Science, and Interdisciplinary Research Center, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gertrud E Morlock
- Chair of Food Science, Institute of Nutritional Science, and Interdisciplinary Research Center, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.
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32
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High-coverage lipidomics for functional lipid and pathway analyses. Anal Chim Acta 2020; 1147:199-210. [PMID: 33485579 DOI: 10.1016/j.aca.2020.11.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 12/19/2022]
Abstract
Rapid advances in front-end separation approaches and analytical technologies have accelerated the development of lipidomics, particularly in terms of increasing analytical coverage to encompass an expanding repertoire of lipids within a single analytical approach. Developments in lipid pathway analysis, however, have somewhat lingered behind, primarily due to (1) the lack of coherent alignment between lipid identifiers in common databases versus that generated from experiments, owing to the differing structural resolution of lipids at molecular level that is specific to the analytical approaches adopted by various laboratories; (2) the immense complexity of lipid metabolic relationships that may entail head group changes, fatty acyls modifications of various forms (e.g. elongation, desaturation, oxidation), as well as active remodeling that demands a multidimensional, panoramic view to take into account all possibilities in lipid pathway analyses. Herein, we discuss current efforts undertaken to address these challenges, as well as alternative form of "pathway analyses" that may be particularly useful for uncovering functional lipid interactions under different biological contexts. Consolidating lipid pathway analyses will be indispensable in facilitating the transition of lipidomics from its prior role of phenotype validation to a hypothesis-generating tool that uncovers novel molecular targets to drive downstream mechanistic pursuits under biomedical settings.
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