1
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Hutchins PD, Saez Cabezas CA, Enokida JS, Hu Y, Lai Y, Mazure V, Martin M, Setula K, Stutzman JR, Wade JH. Monitoring Epoxidized Soybean Oil Degradation Using Liquid Chromatography-Mass Spectrometry and In Silico Spectral Libraries. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1940-1949. [PMID: 39043119 DOI: 10.1021/jasms.4c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Epoxidized soybean oil (ESO) is routinely used as a bioderived plasticizer and stabilizer in polyvinyl chloride (PVC), as it prolongs material integrity during dehydrochlorination. During this process, the epoxide moieties of ESO are progressively converted to chlorohydrins, which amplify ESO's inherent structural complexity. Past characterization efforts utilized separation-mass spectrometry (MS) analysis of the hydrolyzed acyl chains to simplify the complexity. However, this approach significantly increases the complexity of sample preparation and cannot directly monitor the chlorination of individual ESO species during aging. Here, we present a comprehensive LC-MS/MS data acquisition and in silico spectral library identification workflow optimized for intact ESO byproduct analysis. Detailed MS/MS fragmentation rules derived from synthesized standards were coupled with improved fragment ion intensity modeling capabilities to generate a high-fidelity spectral library for rapid ESO byproduct identification. Identification confidence was further bolstered by using retention time modeling to filter spurious MS/MS matches. Finally, we paired this informatic approach with an optimized extraction procedure and reversed-phase separation to generate a detailed timeline of more than 400 ESO species and byproducts during PVC thermal aging. These developments significantly improve our ability to detect, characterize, and understand ESO degradation in complex PVC formulations with new levels of molecular resolution.
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Affiliation(s)
- Paul D Hutchins
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Camila A Saez Cabezas
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Joshua S Enokida
- Packaging & Specialty Plastics, The Dow Chemical Company, 230 Abner Jackson Pkwy, Lake Jackson, Texas 77566, United States
| | - Yushan Hu
- Packaging & Specialty Plastics, The Dow Chemical Company, 230 Abner Jackson Pkwy, Lake Jackson, Texas 77566, United States
| | - Yuming Lai
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Victoria Mazure
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Marie Martin
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - Kelly Setula
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - John R Stutzman
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
| | - James H Wade
- Analytical Science, Core R&D, The Dow Chemical Company, Midland, Michigan 48667, United States
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2
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Martínez S, Albóniga OE, López-Huertas MR, Gradillas A, Barbas C. Reinforcing the Evidence of Mitochondrial Dysfunction in Long COVID Patients Using a Multiplatform Mass Spectrometry-Based Metabolomics Approach. J Proteome Res 2024; 23:3025-3040. [PMID: 38566450 DOI: 10.1021/acs.jproteome.3c00706] [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] [Indexed: 04/04/2024]
Abstract
Despite the recent and increasing knowledge surrounding COVID-19 infection, the underlying mechanisms of the persistence of symptoms for a long time after the acute infection are still not completely understood. Here, a multiplatform mass spectrometry-based approach was used for metabolomic and lipidomic profiling of human plasma samples from Long COVID patients (n = 40) to reveal mitochondrial dysfunction when compared with individuals fully recovered from acute mild COVID-19 (n = 40). Untargeted metabolomic analysis using CE-ESI(+/-)-TOF-MS and GC-Q-MS was performed. Additionally, a lipidomic analysis using LC-ESI(+/-)-QTOF-MS based on an in-house library revealed 447 lipid species identified with a high confidence annotation level. The integration of complementary analytical platforms has allowed a comprehensive metabolic and lipidomic characterization of plasma alterations in Long COVID disease that found 46 relevant metabolites which allowed to discriminate between Long COVID and fully recovered patients. We report specific metabolites altered in Long COVID, mainly related to a decrease in the amino acid metabolism and ceramide plasma levels and an increase in the tricarboxylic acid (TCA) cycle, reinforcing the evidence of an impaired mitochondrial function. The most relevant alterations shown in this study will help to better understand the insights of Long COVID syndrome by providing a deeper knowledge of the metabolomic basis of the pathology.
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Affiliation(s)
- Sara Martínez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities. Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Oihane E Albóniga
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities. Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
- Asociación Centro de Investigación Cooperativa en Biociencias (CICbioGUNE), Bizkaia Science and Technology Park bld 800, 48160 Derio, Bizkaia, Spain
| | - María Rosa López-Huertas
- Unidad de Inmunopatología del SIDA, Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Majadahonda, Spain
| | - Ana Gradillas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities. Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities. Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
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3
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Mouskeftara T, Deda O, Liapikos T, Panteris E, Karagiannidis E, Papazoglou AS, Gika H. Lipidomic-Based Algorithms Can Enhance Prediction of Obstructive Coronary Artery Disease. J Proteome Res 2024; 23:3598-3611. [PMID: 39008891 DOI: 10.1021/acs.jproteome.4c00249] [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] [Indexed: 07/17/2024]
Abstract
Lipidomics emerges as a promising research field with the potential to help in personalized risk stratification and improve our understanding on the functional role of individual lipid species in the metabolic perturbations occurring in coronary artery disease (CAD). This study aimed to utilize a machine learning approach to provide a lipid panel able to identify patients with obstructive CAD. In this posthoc analysis of the prospective CorLipid trial, we investigated the lipid profiles of 146 patients with suspected CAD, divided into two categories based on the existence of obstructive CAD. In total, 517 lipid species were identified, from which 288 lipid species were finally quantified, including glycerophospholipids, glycerolipids, and sphingolipids. Univariate and multivariate statistical analyses have shown significant discrimination between the serum lipidomes of patients with obstructive CAD. Finally, the XGBoost algorithm identified a panel of 17 serum biomarkers (5 sphingolipids, 7 glycerophospholipids, a triacylglycerol, galectin-3, glucose, LDL, and LDH) as totally sensitive (100% sensitivity, 62.1% specificity, 100% negative predictive value) for the prediction of obstructive CAD. Our findings shed light on dysregulated lipid metabolism's role in CAD, validating existing evidence and suggesting promise for novel therapies and improved risk stratification.
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Affiliation(s)
- Thomai Mouskeftara
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Biomic_AUTh, CIRI-AUTH Center for Interdisciplinary Research and Innovation Aristotle University of Thessaloniki, 57001 Thessaloniki, Greece
| | - Olga Deda
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Biomic_AUTh, CIRI-AUTH Center for Interdisciplinary Research and Innovation Aristotle University of Thessaloniki, 57001 Thessaloniki, Greece
| | - Theodoros Liapikos
- Biomic_AUTh, CIRI-AUTH Center for Interdisciplinary Research and Innovation Aristotle University of Thessaloniki, 57001 Thessaloniki, Greece
| | - Eleftherios Panteris
- Biomic_AUTh, CIRI-AUTH Center for Interdisciplinary Research and Innovation Aristotle University of Thessaloniki, 57001 Thessaloniki, Greece
| | - Efstratios Karagiannidis
- Second Department of Cardiology, General Hospital "Hippokration", Aristotle University of Thessaloniki, Konstantinoupoleos 49, 54642 Thessaloniki, Greece
| | | | - Helen Gika
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
- Biomic_AUTh, CIRI-AUTH Center for Interdisciplinary Research and Innovation Aristotle University of Thessaloniki, 57001 Thessaloniki, Greece
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4
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Isom M, Desaire H. Skin Surface Sebum Analysis by ESI-MS. Biomolecules 2024; 14:790. [PMID: 39062504 PMCID: PMC11274890 DOI: 10.3390/biom14070790] [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: 06/11/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
The skin surface is an important sample source that the metabolomics community has only just begun to explore. Alterations in sebum, the lipid-rich mixture coating the skin surface, correlate with age, sex, ethnicity, diet, exercise, and disease state, making the skin surface an ideal sample source for future noninvasive biomarker exploration, disease diagnosis, and forensic investigation. The potential of sebum sampling has been realized primarily via electrospray ionization mass spectrometry (ESI-MS), an ideal approach to assess the skin surface lipidome. However, a better understanding of sebum collection and subsequent ESI-MS analysis is required before skin surface sampling can be implemented in routine analyses. Challenges include ambiguity in definitive lipid identification, inherent biological variability in sebum production, and methodological, technical variability in analyses. To overcome these obstacles, avoid common pitfalls, and achieve reproducible, robust outcomes, every portion of the workflow-from sample collection to data analysis-should be carefully considered with the specific application in mind. This review details current practices in sebum sampling, sample preparation, ESI-MS data acquisition, and data analysis, and it provides important considerations in acquiring meaningful lipidomic datasets from the skin surface. Forensic researchers investigating sebum as a means for suspect elimination in lieu of adequate fingerprint ridge detail or database matches, as well as clinical researchers interested in noninvasive biomarker exploration, disease diagnosis, and treatment monitoring, can use this review as a guide for developing methods of best-practice.
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Affiliation(s)
| | - Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA;
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5
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Tsugawa H, Ishihara T, Ogasa K, Iwanami S, Hori A, Takahashi M, Yamada Y, Satoh-Takayama N, Ohno H, Minoda A, Arita M. A lipidome landscape of aging in mice. NATURE AGING 2024; 4:709-726. [PMID: 38609525 DOI: 10.1038/s43587-024-00610-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/07/2024] [Indexed: 04/14/2024]
Abstract
Understanding the molecular mechanisms of aging is crucial for enhancing healthy longevity. We conducted untargeted lipidomics across 13 biological samples from mice at various life stages (2, 12, 19 and 24 months) to explore the potential link between aging and lipid metabolism, considering sex (male or female) and microbiome (specific pathogen-free or germ-free) dependencies. By analyzing 2,704 molecules from 109 lipid subclasses, we characterized common and tissue-specific lipidome alterations associated with aging. For example, the levels of bis(monoacylglycero)phosphate containing polyunsaturated fatty acids increased in various organs during aging, whereas the levels of other phospholipids containing saturated and monounsaturated fatty acids decreased. In addition, we discovered age-dependent sulfonolipid accumulation, absent in germ-free mice, correlating with Alistipes abundance determined by 16S ribosomal RNA gene amplicon sequencing. In the male kidney, glycolipids such as galactosylceramides, galabiosylceramides (Gal2Cer), trihexosylceramides (Hex3Cer), and mono- and digalactosyldiacylglycerols were detected, with two lipid classes-Gal2Cer and Hex3Cer-being significantly enriched in aged mice. Integrated analysis of the kidney transcriptome revealed uridine diphosphate galactosyltransferase 8A (UGT8a), alkylglycerone phosphate synthase and fatty acyl-coenzyme A reductase 1 as potential enzymes responsible for the male-specific glycolipid biosynthesis in vivo, which would be relevant to sex dependency in kidney diseases. Inhibiting UGT8 reduced the levels of these glycolipids and the expression of inflammatory cytokines in the kidney. Our study provides a valuable resource for clarifying potential links between lipid metabolism and aging.
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Affiliation(s)
- Hiroshi Tsugawa
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Molecular and Cellular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
| | - Tomoaki Ishihara
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Pharmacy, Nagasaki International University, Sasebo, Japan
| | - Kota Ogasa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Seigo Iwanami
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Aya Hori
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mikiko Takahashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yutaka Yamada
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Naoko Satoh-Takayama
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aki Minoda
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Molecular and Cellular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan.
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan.
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6
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Robeyns R, Sisto A, Iturrospe E, da Silva KM, van de Lavoir M, Timmerman V, Covaci A, Stroobants S, van Nuijs ALN. The Metabolic and Lipidomic Fingerprint of Torin1 Exposure in Mouse Embryonic Fibroblasts Using Untargeted Metabolomics. Metabolites 2024; 14:248. [PMID: 38786725 PMCID: PMC11123261 DOI: 10.3390/metabo14050248] [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: 04/04/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Torin1, a selective kinase inhibitor targeting the mammalian target of rapamycin (mTOR), remains widely used in autophagy research due to its potent autophagy-inducing abilities, regardless of its unspecific properties. Recognizing the impact of mTOR inhibition on metabolism, our objective was to develop a reliable and thorough untargeted metabolomics workflow to study torin1-induced metabolic changes in mouse embryonic fibroblast (MEF) cells. Crucially, our quality assurance and quality control (QA/QC) protocols were designed to increase confidence in the reported findings by reducing the likelihood of false positives, including a validation experiment replicating all experimental steps from sample preparation to data analysis. This study investigated the metabolic fingerprint of torin1 exposure by using liquid chromatography-high resolution mass spectrometry (LC-HRMS)-based untargeted metabolomics platforms. Our workflow identified 67 altered metabolites after torin1 exposure, combining univariate and multivariate statistics and the implementation of a validation experiment. In particular, intracellular ceramides, diglycerides, phosphatidylcholines, phosphatidylethanolamines, glutathione, and 5'-methylthioadenosine were downregulated. Lyso-phosphatidylcholines, lyso-phosphatidylethanolamines, glycerophosphocholine, triglycerides, inosine, and hypoxanthine were upregulated. Further biochemical pathway analyses provided deeper insights into the reported changes. Ultimately, our study provides a valuable workflow that can be implemented for future investigations into the effects of other compounds, including more specific autophagy modulators.
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Affiliation(s)
- Rani Robeyns
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Angela Sisto
- Peripheral Neuropathy Research Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Elias Iturrospe
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | | | - Maria van de Lavoir
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Adrian Covaci
- Toxicological Centre, University of Antwerp, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Sigrid Stroobants
- Department of Nuclear Medicine, Antwerp University Hospital, 2650 Antwerp, Belgium
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7
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Fernandez Requena B, Gonzalez-Riano C, Barbas C. Addressing the untargeted lipidomics challenge in urine samples: Comparative study of extraction methods by UHPLC-ESI-QTOF-MS. Anal Chim Acta 2024; 1299:342433. [PMID: 38499427 DOI: 10.1016/j.aca.2024.342433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Urine analysis has remained a fundamental and widely used method in clinical diagnostics for over a century. With its minimal invasive nature and comprehensive range of analytes, urine has established itself as a clinical diagnostic tool for various disorders, including renal, urological, metabolic, and endocrine diseases. Furthermore, urine's unique attributes make it an attractive matrix for biomarker discovery, as well as in assessing the metabolic and physiological states of patients and healthy individuals alike. However, limitations in our knowledge of average values and sources of urinary lipids decrease the wider clinical application of urinary lipidomics. In this context, untargeted lipidomics analysis relies heavily on the extraction and analysis of lipids in biological samples. Nevertheless, this type of analysis presents challenges in lipid identification due to the diverse nature of lipids. Therefore, proper sample treatment before analysis is crucial to obtain robust and reproducible lipidomic profiles. To address this gap, we conducted a comparative study of a urine pool sample collected from twenty healthy volunteers using four different lipid extraction methods: one biphasic and three monophasic protocols. The extracted lipids were then analyzed using UHPLC-MS and MS/MS, and the semi-quantification of all the accurately annotated lipid species was performed for each extraction method.
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Affiliation(s)
- Belen Fernandez Requena
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España
| | - Carolina Gonzalez-Riano
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España.
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8
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Xu R, Liu H, Yuan F, Kim S, Kirpich I, McClain CJ, Zhang X. Lipid Wizard: Analysis Software for Comprehensive Two-Dimensional Liquid Chromatography-Mass Spectrometry-Based Lipid Profiling. Anal Chem 2024; 96:5375-5383. [PMID: 38523323 DOI: 10.1021/acs.analchem.3c04419] [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] [Indexed: 03/26/2024]
Abstract
Lipids play a significant role in life activities and participate in the biological system through different pathways. Although comprehensive two-dimensional liquid chromatography-mass spectrometry (2DLC-MS) has been developed to profile lipid abundance changes, lipid identification and quantification from 2DLC-MS data remain a challenge. We created Lipid Wizard, open-source software for lipid assignment and isotopic peak stripping of the 2DLC-MS data. Lipid Wizard takes the peak list deconvoluted from the 2DLC-MS data as input and assigns each isotopic peak to the lipids recorded in the LIPID MAPS database by precursor ion m/z matching. The matched lipids are then filtered by the first-dimension retention time (1D RT), followed by the second-dimension retention time (2D RT), where the 2D RT of each lipid is predicted using an equivalent carbon number (ECN) model. The remaining assigned lipids are used for isotopic peak stripping via an iterative linear regression. The performance of Lipid Wizard was tested using a set of lipid standards and then applied to study the lipid changes in the livers of mice (fat-1) fed with alcohol.
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Affiliation(s)
- Raobo Xu
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
| | - Huan Liu
- Department of Computer Science and Engineering, University of Louisville, Louisville, Kentucky 40292, United States
| | - Fang Yuan
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
| | - Seongho Kim
- Department of Oncology, Wayne State University, Detroit, Michigan 48201, United States
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan 48201, United States
| | - Irina Kirpich
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky 40292, United States
| | - Craig J McClain
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, United States
- Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky 40206, United States
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, Kentucky 40292, United States
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, United States
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9
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Goracci L, Tiberi P, Di Bona S, Bonciarelli S, Passeri GI, Piroddi M, Moretti S, Volpi C, Zamora I, Cruciani G. MARS: A Multipurpose Software for Untargeted LC-MS-Based Metabolomics and Exposomics. Anal Chem 2024; 96:1468-1477. [PMID: 38236168 PMCID: PMC10831794 DOI: 10.1021/acs.analchem.3c03620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 12/24/2023] [Accepted: 12/29/2023] [Indexed: 01/19/2024]
Abstract
Untargeted metabolomics is a growing field, in which recent advances in high-resolution mass spectrometry coupled with liquid chromatography (LC-MS) have facilitated untargeted approaches as a result of improvements in sensitivity, mass accuracy, and resolving power. However, a very large amount of data are generated. Consequently, using computational tools is now mandatory for the in-depth analysis of untargeted metabolomics data. This article describes MetAbolomics ReSearch (MARS), an all-in-one vendor-agnostic graphical user interface-based software applying LC-MS analysis to untargeted metabolomics. All of the analytical steps are described (from instrument data conversion and processing to statistical analysis, annotation/identification, quantification, and preliminary biological interpretation), and tools developed to improve annotation accuracy (e.g., multiple adducts and in-source fragmentation detection, trends across samples, and the MS/MS validator) are highlighted. In addition, MARS allows in-house building of reference databases, to bypass the limits of freely available MS/MS spectra collections. Focusing on the flexibility of the software and its user-friendliness, which are two important features in multipurpose software, MARS could provide new perspectives in untargeted metabolomics data analysis.
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Affiliation(s)
- Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, Universita degli Studi di Perugia, via Elce di Sotto 8, Perugia 06123, Italy
| | - Paolo Tiberi
- Molecular
Discovery Ltd., Centennial
Park, Borehamwood, Hertfordshire WD6 4PJ, U.K.
| | - Stefano Di Bona
- Molecular
Horizon, Via Montelino,
30, Bettona (PG) 06084, Italy
| | - Stefano Bonciarelli
- Molecular
Discovery Ltd., Centennial
Park, Borehamwood, Hertfordshire WD6 4PJ, U.K.
| | | | - Marta Piroddi
- Molecular
Horizon, Via Montelino,
30, Bettona (PG) 06084, Italy
| | - Simone Moretti
- Molecular
Horizon, Via Montelino,
30, Bettona (PG) 06084, Italy
| | - Claudia Volpi
- Department
of Medicine and Surgery, P.le Gambuli 1, Perugia 06129, Italy
| | - Ismael Zamora
- Mass
Analytica, Rambla de
celler 113, Sant Cugat del Vallés 08173, Spain
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, Universita degli Studi di Perugia, via Elce di Sotto 8, Perugia 06123, Italy
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10
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Lei J, He Y, Zhu S, Shi J, Tan CP, Liu Y, Xu YJ. SpecLipIDA: a pseudotargeted lipidomics approach for polyunsaturated fatty acids in milk. Analyst 2024; 149:751-760. [PMID: 38194259 DOI: 10.1039/d3an01536j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Polyunsaturated fatty acids (PUFAs), such as arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), play an important role in the nutritional value of milk lipids. However, a comprehensive analysis of PUFAs and their esters in milk is still scarce. In this study, we developed a novel pseudotargeted lipidomics approach, named SpecLipIDA, for determining PUFA lipids in milk. Triglycerides (TGs) and phospholipids (PLs) were separated using NH2 cartridges, and mass spectrometry data in the information-dependent acquisition (IDA) mode were preprocessed by MS-DIAL, leading to improved identification in subsequent targeted analysis. The target matching algorithm, based on specific lipid cleavage patterns, demonstrated enhanced identification of PUFA lipids compared to the lipid annotations provided by MS-DIAL and GNPS. The approach was applied to identify PUFA lipids in various milk samples, resulting in the detection of a total of 115 PUFA lipids. The results revealed distinct differences in PUFA lipids among different samples, with 44 PUFA lipids significantly contributing to these differences. Our study indicated that SpecLipIDA is an efficient method for rapidly and specifically screening PUFA lipids.
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Affiliation(s)
- Jingnan Lei
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, No. 1800 Lihu Road, Binhu District, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Yuan He
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, No. 1800 Lihu Road, Binhu District, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Shuang Zhu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, No. 1800 Lihu Road, Binhu District, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Jiachen Shi
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, No. 1800 Lihu Road, Binhu District, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Chin-Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, University Putra Malaysia, Selangor 410500, Malaysia
| | - Yuanfa Liu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, No. 1800 Lihu Road, Binhu District, Wuxi, Jiangsu 214122, People's Republic of China.
| | - Yong-Jiang Xu
- State Key Laboratory of Food Science and Resources, School of Food Science and Technology, Jiangnan University, No. 1800 Lihu Road, Binhu District, Wuxi, Jiangsu 214122, People's Republic of China.
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11
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Fernández Requena B, Nadeem S, Reddy VP, Naidoo V, Glasgow JN, Steyn AJC, Barbas C, Gonzalez-Riano C. LiLA: lipid lung-based ATLAS built through a comprehensive workflow designed for an accurate lipid annotation. Commun Biol 2024; 7:45. [PMID: 38182666 PMCID: PMC10770321 DOI: 10.1038/s42003-023-05680-7] [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: 08/17/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However, annotating the wide variety of lipid species in biological samples remains challenging in untargeted lipidomic studies. In this work, we present a lipid annotation workflow based on LC-MS and MS/MS strategies, the combination of four bioinformatic tools, and a decision tree to support the accurate annotation and semi-quantification of the lipid species present in lung tissue from control mice. The proposed workflow allowed us to generate a lipid lung-based ATLAS (LiLA), which was then employed to unveil the lipidomic signatures of the Mycobacterium tuberculosis infection at two different time points for a deeper understanding of the disease progression. This workflow, combined with manual inspection strategies of MS/MS data, can enhance the annotation process for lipidomic studies and guide the generation of sample-specific lipidome maps. LiLA serves as a freely available data resource that can be employed in future studies to address lipidomic alterations in mice lung tissue.
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Affiliation(s)
- Belén Fernández Requena
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España
| | - Sajid Nadeem
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vineel P Reddy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Joel N Glasgow
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adrie J C Steyn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Africa Health Research Institute, Durban, South Africa
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España.
| | - Carolina Gonzalez-Riano
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España.
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12
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Wei J, Wong LC, Boland S. Lipids as Emerging Biomarkers in Neurodegenerative Diseases. Int J Mol Sci 2023; 25:131. [PMID: 38203300 PMCID: PMC10778656 DOI: 10.3390/ijms25010131] [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: 08/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Biomarkers are molecules that can be used to observe changes in an individual's biochemical or medical status and provide information to aid diagnosis or treatment decisions. Dysregulation in lipid metabolism in the brain is a major risk factor for many neurodegenerative disorders, including frontotemporal dementia, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Thus, there is a growing interest in using lipids as biomarkers in neurodegenerative diseases, with the anionic phospholipid bis(monoacylglycerol)phosphate and (glyco-)sphingolipids being the most promising lipid classes thus far. In this review, we provide a general overview of lipid biology, provide examples of abnormal lysosomal lipid metabolism in neurodegenerative diseases, and discuss how these insights might offer novel and promising opportunities in biomarker development and therapeutic discovery. Finally, we discuss the challenges and opportunities of lipid biomarkers and biomarker panels in diagnosis, prognosis, and/or treatment response in the clinic.
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13
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Chamoso-Sanchez D, Rabadán Pérez F, Argente J, Barbas C, Martos-Moreno GA, Rupérez FJ. Identifying subgroups of childhood obesity by using multiplatform metabotyping. Front Mol Biosci 2023; 10:1301996. [PMID: 38174068 PMCID: PMC10761426 DOI: 10.3389/fmolb.2023.1301996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction: Obesity results from an interplay between genetic predisposition and environmental factors such as diet, physical activity, culture, and socioeconomic status. Personalized treatments for obesity would be optimal, thus necessitating the identification of individual characteristics to improve the effectiveness of therapies. For example, genetic impairment of the leptin-melanocortin pathway can result in rare cases of severe early-onset obesity. Metabolomics has the potential to distinguish between a healthy and obese status; however, differentiating subsets of individuals within the obesity spectrum remains challenging. Factor analysis can integrate patient features from diverse sources, allowing an accurate subclassification of individuals. Methods: This study presents a workflow to identify metabotypes, particularly when routine clinical studies fail in patient categorization. 110 children with obesity (BMI > +2 SDS) genotyped for nine genes involved in the leptin-melanocortin pathway (CPE, MC3R, MC4R, MRAP2, NCOA1, PCSK1, POMC, SH2B1, and SIM1) and two glutamate receptor genes (GRM7 and GRIK1) were studied; 55 harboring heterozygous rare sequence variants and 55 with no variants. Anthropometric and routine clinical laboratory data were collected, and serum samples processed for untargeted metabolomic analysis using GC-q-MS and CE-TOF-MS and reversed-phase U(H)PLC-QTOF-MS/MS in positive and negative ionization modes. Following signal processing and multialignment, multivariate and univariate statistical analyses were applied to evaluate the genetic trait association with metabolomics data and clinical and routine laboratory features. Results and Discussion: Neither the presence of a heterozygous rare sequence variant nor clinical/routine laboratory features determined subgroups in the metabolomics data. To identify metabolomic subtypes, we applied Factor Analysis, by constructing a composite matrix from the five analytical platforms. Six factors were discovered and three different metabotypes. Subtle but neat differences in the circulating lipids, as well as in insulin sensitivity could be established, which opens the possibility to personalize the treatment according to the patients categorization into such obesity subtypes. Metabotyping in clinical contexts poses challenges due to the influence of various uncontrolled variables on metabolic phenotypes. However, this strategy reveals the potential to identify subsets of patients with similar clinical diagnoses but different metabolic conditions. This approach underscores the broader applicability of Factor Analysis in metabotyping across diverse clinical scenarios.
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Affiliation(s)
- David Chamoso-Sanchez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | | | - Jesús Argente
- Department of Pediatrics and Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Instituto de Investigación Sanitaria La Princesa, Universidad Autónoma de Madrid, Madrid, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
- IMDEA Food Institute, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
| | - Gabriel A. Martos-Moreno
- Department of Pediatrics and Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Instituto de Investigación Sanitaria La Princesa, Universidad Autónoma de Madrid, Madrid, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Francisco J. Rupérez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Boadilla del Monte, Spain
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14
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Cajka T, Hricko J, Rudl Kulhava L, Paucova M, Novakova M, Fiehn O, Kuda O. Exploring the Impact of Organic Solvent Quality and Unusual Adduct Formation during LC-MS-Based Lipidomic Profiling. Metabolites 2023; 13:966. [PMID: 37755246 PMCID: PMC10536874 DOI: 10.3390/metabo13090966] [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: 08/03/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is the key technique for analyzing complex lipids in biological samples. Various LC-MS modes are used for lipid separation, including different stationary phases, mobile-phase solvents, and modifiers. Quality control in lipidomics analysis is crucial to ensuring the generated data's reliability, reproducibility, and accuracy. While several quality control measures are commonly discussed, the impact of organic solvent quality during LC-MS analysis is often overlooked. Additionally, the annotation of complex lipids remains prone to biases, leading to potential misidentifications and incomplete characterization of lipid species. In this study, we investigate how LC-MS-grade isopropanol from different vendors may influence the quality of the mobile phase used in LC-MS-based untargeted lipidomic profiling of biological samples. Furthermore, we report the occurrence of an unusual, yet highly abundant, ethylamine adduct [M+46.0651]+ that may form for specific lipid subclasses during LC-MS analysis in positive electrospray ionization mode when acetonitrile is part of the mobile phase, potentially leading to lipid misidentification. These findings emphasize the importance of considering solvent quality in LC-MS analysis and highlight challenges in lipid annotation.
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Affiliation(s)
- Tomas Cajka
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Jiri Hricko
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Lucie Rudl Kulhava
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Michaela Paucova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Michaela Novakova
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA;
| | - Ondrej Kuda
- Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic; (J.H.); (L.R.K.); (M.P.); (M.N.); (O.K.)
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15
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Iturrospe E, Robeyns R, da Silva KM, van de Lavoir M, Boeckmans J, Vanhaecke T, van Nuijs ALN, Covaci A. Metabolic signature of HepaRG cells exposed to ethanol and tumor necrosis factor alpha to study alcoholic steatohepatitis by LC-MS-based untargeted metabolomics. Arch Toxicol 2023; 97:1335-1353. [PMID: 36826472 DOI: 10.1007/s00204-023-03470-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/16/2023] [Indexed: 02/25/2023]
Abstract
Despite the high prevalence of alcoholic liver disease, its identification and characterization remain poor, especially in early stages such as alcoholic fatty liver disease and alcoholic steatohepatitis. This latter implies diagnostic difficulties, few therapeutic options and unclear mechanisms of action. To elucidate the metabolic alterations and pinpoint affected biochemical pathways, alcoholic steatohepatitis was simulated in vitro by exposing HepaRG cells to ethanol (IC10, 368 mM) and tumor necrosis factor alpha (TNF-α, 50 ng/mL) for 24 h. This combined exposure was compared to solely ethanol-exposed as well as -nonexposed cells. Four different metabolomics platforms were used combining liquid chromatography, high-resolution mass spectrometry and drift tube ion mobility to elucidate both intracellular and extracellular metabolic alterations. Some of the key findings include the influence of TNF-α in the upregulation of hepatic triglycerides and the downregulation of hepatic phosphatidylethanolamines and phosphatidylcholines. S-Adenosylmethionine showed to play a central role in the progression of alcoholic steatohepatitis. In addition, fatty acyl esters of hydroxy fatty acid (FAHFA)-containing triglycerides were detected for the first time in human hepatocytes and their alterations showed a potentially important role during the progression of alcoholic steatohepatitis. Ethoxylated phosphorylcholine was identified as a potential new biomarker of ethanol exposure.
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Affiliation(s)
- Elias Iturrospe
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Jette, Belgium.
| | - Rani Robeyns
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | | | - Maria van de Lavoir
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Joost Boeckmans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Jette, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Jette, Belgium
| | | | - Adrian Covaci
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.
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16
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Gertner DS, Violi JP, Bishop DP, Padula MP. Lipid Spectrum Generator: A Simple Script for the Generation of Accurate In Silico Lipid Fragmentation Spectra. Anal Chem 2023; 95:2909-2916. [PMID: 36692449 DOI: 10.1021/acs.analchem.2c04518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Due to the complexity of lipids in nature, the use of in silico generated spectral libraries to identify lipid species from mass spectral data has become an integral part of many lipidomic workflows. However, many in silico libraries are either limited in usability or their capacity to represent lipid species. Here, we introduce Lipid Spectrum Generator, an open-source in silico spectral library generator specifically designed to aid in the identification of lipids in liquid chromatography-tandem mass spectrometry analysis.
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Affiliation(s)
- David S Gertner
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Jake P Violi
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - David P Bishop
- School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
| | - Matthew P Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, University of Technology Sydney, Ultimo 2007, Australia
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17
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Ni Z, Wölk M, Jukes G, Mendivelso Espinosa K, Ahrends R, Aimo L, Alvarez-Jarreta J, Andrews S, Andrews R, Bridge A, Clair GC, Conroy MJ, Fahy E, Gaud C, Goracci L, Hartler J, Hoffmann N, Kopczyinki D, Korf A, Lopez-Clavijo AF, Malik A, Ackerman JM, Molenaar MR, O'Donovan C, Pluskal T, Shevchenko A, Slenter D, Siuzdak G, Kutmon M, Tsugawa H, Willighagen EL, Xia J, O'Donnell VB, Fedorova M. Guiding the choice of informatics software and tools for lipidomics research applications. Nat Methods 2023; 20:193-204. [PMID: 36543939 PMCID: PMC10263382 DOI: 10.1038/s41592-022-01710-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/02/2022] [Indexed: 12/24/2022]
Abstract
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.
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Affiliation(s)
- Zhixu Ni
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Michele Wölk
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | - Geoff Jukes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Lucila Aimo
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Jorge Alvarez-Jarreta
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Simon Andrews
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Robert Andrews
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Alan Bridge
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Geremy C Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew J Conroy
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Eoin Fahy
- Department of Bioengineering, University of California, San Diego, CA, USA
| | - Caroline Gaud
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealthe-University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Dominik Kopczyinki
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Ansgar Korf
- Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | | | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Martijn R Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claire O'Donovan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Denise Slenter
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA, USA
| | - Martina Kutmon
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Hiroshi Tsugawa
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Egon L Willighagen
- Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Canada
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK.
| | - Maria Fedorova
- Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.
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18
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Computational mass spectrometry accelerates C = C position-resolved untargeted lipidomics using oxygen attachment dissociation. Commun Chem 2022; 5:162. [PMID: 36698019 PMCID: PMC9814143 DOI: 10.1038/s42004-022-00778-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry-based untargeted lipidomics has revealed the lipidome atlas of living organisms at the molecular species level. Despite the double bond (C = C) position being a crucial factor in biological system, the C = C defined structures have not yet been characterized comprehensively. Here, we present an approach for C = C position-resolved untargeted lipidomics using a combination of oxygen attachment dissociation and computational mass spectrometry to increase the annotation rate. We validated the accuracy of our platform as per the authentic standards of 85 lipids and the biogenic standards of 52 molecules containing polyunsaturated fatty acids (PUFAs) from the cultured cells fed with various fatty acid-enriched media. By analyzing human and mice-derived samples, we characterized 648 unique lipids with the C = C position-resolved level encompassing 24 lipid subclasses defined by LIPIDMAPS. Our platform also illuminated the unique profiles of tissue-specific lipids containing n-3 and/or n-6 very long-chain PUFAs (carbon [Formula: see text] 28 and double bonds [Formula: see text] 4) in the eye, testis, and brain of the mouse.
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19
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Variations in the milk lipidomes of two dairy cow herds fed hay- or silage-based diets over a full year. Food Chem 2022; 390:133091. [DOI: 10.1016/j.foodchem.2022.133091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/15/2022] [Accepted: 04/24/2022] [Indexed: 11/17/2022]
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20
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Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022; 12:metabo12070584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [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: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
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Affiliation(s)
- Nils Hoffmann
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), 52425 Jülich, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
| | - Gerhard Mayer
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany;
| | - Canan Has
- Biological Mass Spectrometry, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- CENTOGENE GmbH, 18055 Rostock, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Fadi Al Machot
- Faculty of Science and Technology, Norwegian University for Life Science (NMBU), 1433 Ås, Norway;
| | - Dominik Schwudke
- Bioanalytical Chemistry, Forschungszentrum Borstel, Leibniz Lung Center, 23845 Borstel, Germany;
- Airway Research Center North, German Center for Lung Research (DZL), 23845 Borstel, Germany
- German Center for Infection Research (DZIF), TTU Tuberculosis, 23845 Borstel, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Katrin Marcus
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
| | - Martin Eisenacher
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, 85764 Neuherberg, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
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21
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da Silva KM, Iturrospe E, van den Boom R, van de Lavoir M, Robeyns R, Vergauwen L, Knapen D, Cuykx M, Covaci A, van Nuijs ALN. Lipidomics profiling of zebrafish liver through untargeted liquid chromatography-high resolution mass spectrometry. J Sep Sci 2022; 45:2935-2945. [PMID: 35716100 DOI: 10.1002/jssc.202200214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 06/13/2022] [Accepted: 06/13/2022] [Indexed: 11/10/2022]
Abstract
Lipidomics analysis of zebrafish tissues has shown promising results to understand disease-related outcomes of exposure to toxic substances at molecular level. However, knowledge about their lipidome is limited, as most untargeted studies only identify the lipids that are statistically significant in their setup. In this work, liquid chromatography-high resolution mass spectrometry was used to study different aspects of the analytical workflow, i.e., extraction solvents (methanol/chloroform/water (3/2/2, v/v/v), methanol/dichloromethane/water (2/3/2, v/v/v) and methanol/methyl-tert-butyl ether/water (3/10/2.5, v/v/v), instrumental response, and strategies used for lipid annotation. The number of high-quality features (relative standard deviation of the intensity values ≤ 10% in the range 103 -107 counts) was affected by the dilution of lipid extracts, indicating that it is an important parameter for developing untargeted methods. The workflows used allowed the selection of a dilution factor to annotate 712 lipid species (507 bulk lipids) in zebrafish liver using four software (LipidMatch, LipidHunter, MS-DIAL and Lipostar). Retention time mapping was a valuable tool to filter lipid annotations obtained from automatic software annotations. The lipid profiling of zebrafish livers will help in a better understanding of the true constitution of their lipidome at the species level, as well as in the use of zebrafish in toxicological studies. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Katyeny Manuela da Silva
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Elias Iturrospe
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium.,Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Campus Jette, Vrije Universiteit Brussels, Laarbeeklaan 103, Brussels, 1090, Belgium
| | - Rik van den Boom
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Maria van de Lavoir
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Rani Robeyns
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Lucia Vergauwen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Matthias Cuykx
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium.,Department of Laboratory Medicine AZ Turnhout, Rubenslaan 166, Turnhout, 2300, Belgium
| | - Adrian Covaci
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
| | - Alexander L N van Nuijs
- Toxicological Centre, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, Antwerp, 2610, Belgium
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22
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Abreu S, Héron S, Solgadi A, Prost B, Dalloux-Chioccioli J, Kermarrec A, Meynier A, Bertrand-Michel J, Tchapla A, Chaminade P. Rapid assessment of fatty acyls chains of phospholipids and plasmalogens by atmospheric pressure chemical ionization in positive mode and high-resolution mass spectrometry using in-source generated monoacylglycerol like fragments intensities. J Chromatogr A 2022; 1673:463093. [DOI: 10.1016/j.chroma.2022.463093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 10/18/2022]
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23
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Iturrospe E, da Silva KM, Robeyns R, van de Lavoir M, Boeckmans J, Vanhaecke T, van Nuijs ALN, Covaci A. Metabolic Signature of Ethanol-Induced Hepatotoxicity in HepaRG Cells by Liquid Chromatography-Mass Spectrometry-Based Untargeted Metabolomics. J Proteome Res 2022; 21:1153-1166. [PMID: 35274962 DOI: 10.1021/acs.jproteome.2c00029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alcoholic liver disease is highly prevalent but poorly identified and characterized, leading to knowledge gaps, which impairs early diagnosis. Excessive alcohol consumption is known to alter lipid metabolism, followed by progressive intracellular lipid accumulation, resulting in alcoholic fatty liver disease. In this study, HepaRG cells were exposed to ethanol at IC10 and 1/10 IC10 for 24 and 48 h. Metabolic alterations were investigated intra- and extracellularly with liquid chromatography-high-resolution mass spectrometry. Ion mobility was added as an extra separation dimension for untargeted lipidomics to improve annotation confidence. Distinctive patterns between exposed and control cells were consistently observed, with intracellular upregulation of di- and triglycerides, downregulation of phosphatidylcholines and phosphatidylethanolamines, sphingomyelins, and S-adenosylmethionine, among others. Several intracellular metabolic patterns could be related to changes in the extracellular environment, such as increased intracellular hydrolysis of sphingomyelins, leading to increased phosphorylcholine secretion. Carnitines showed alterations depending on the size of their carbon chain, which highlights the interplay between β-oxidation in mitochondria and peroxisomes. Potential new biomarkers of ethanol-induced hepatotoxicity have been observed, such as ceramides with a sphingadienine backbone, octanoylcarnitine, creatine, acetylcholine, and ethoxylated phosphorylcholine. The combination of the metabolic fingerprint and footprint enabled a comprehensive investigation of the pathophysiology behind ethanol-induced hepatotoxicity.
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Affiliation(s)
- Elias Iturrospe
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.,Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | | | - Rani Robeyns
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Maria van de Lavoir
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
| | - Joost Boeckmans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | | | - Adrian Covaci
- Toxicological Centre, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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24
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Sochorová M, Vávrová K, Fedorova M, Ni Z, Slenter D, Kutmon M, Willighagen EL, Letsiou S, Töröcsik D, Marchetti-Deschmann M, Zoratto S, Kremslehner C, Gruber F. Research Techniques Made Simple: Lipidomic Analysis in Skin Research. J Invest Dermatol 2021; 142:4-11.e1. [PMID: 34924150 DOI: 10.1016/j.jid.2021.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022]
Abstract
Although lipids are crucial molecules for cell structure, metabolism, and signaling in most organs, they have additional specific functions in the skin. Lipids are required for the maintenance and regulation of the epidermal barrier, physical properties of the skin, and defense against microbes. Analysis of the lipidome-the totality of lipids-is of similar complexity to those of proteomics or other omics, with lipid structures ranging from simple, linear, to highly complex structures. In addition, the ordering and chemical modifications of lipids have consequences on their biological function, especially in the skin. Recent advances in analytic capability (usually with mass spectrometry), bioinformatic processing, and integration with other dermatological big data have allowed researchers to increasingly understand the roles of specific lipid species in skin biology. In this paper, we review the techniques used to analyze skin lipidomics and epilipidomics.
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Affiliation(s)
- Michaela Sochorová
- Department of Dermatology, Medical University of Vienna, Vienna, Austria; Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria; Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Kateřina Vávrová
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, Leipzig, Germany; Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Leipzig University, Leipzig, Germany; Center for Biotechnology and Biomedicine (BBZ), Leipzig University, Leipzig, Germany
| | - Denise Slenter
- Department of Bioinformatics (BiGCaT), NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Martina Kutmon
- Department of Bioinformatics (BiGCaT), NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - Egon L Willighagen
- Department of Bioinformatics (BiGCaT), NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Sophia Letsiou
- Department of Metabolic Diseases, University Medical Center Utrecht, Utrecht, Netherlands
| | - Daniel Töröcsik
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Martina Marchetti-Deschmann
- Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria; Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Vienna, Austria; Austrian Cluster of Tissue Regeneration, Vienna, Austria
| | - Samuele Zoratto
- Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria; Institute of Chemical Technologies and Analytics, TU Wien (Vienna University of Technology), Vienna, Austria; Austrian Cluster of Tissue Regeneration, Vienna, Austria
| | - Christopher Kremslehner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria; Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria
| | - Florian Gruber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria; Christian Doppler Laboratory for Skin Multimodal Analytical Imaging of Aging and Senescence (SKINMAGINE), Medical University of Vienna, Vienna, Austria.
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25
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The Hitchhiker's Guide to Untargeted Lipidomics Analysis: Practical Guidelines. Metabolites 2021; 11:metabo11110713. [PMID: 34822371 PMCID: PMC8624948 DOI: 10.3390/metabo11110713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 11/30/2022] Open
Abstract
Lipidomics is a newly emerged discipline involving the identification and quantification of thousands of lipids. As a part of the omics field, lipidomics has shown rapid growth both in the number of studies and in the size of lipidome datasets, thus, requiring specific and efficient data analysis approaches. This paper aims to provide guidelines for analyzing and interpreting lipidome data obtained using untargeted methods that rely on liquid chromatography coupled with mass spectrometry (LC-MS) to detect and measure the intensities of lipid compounds. We present a state-of-the-art untargeted LC-MS workflow for lipidomics, from study design to annotation of lipid features, focusing on practical, rather than theoretical, approaches for data analysis, and we outline possible applications of untargeted lipidomics for biological studies. We provide a detailed R notebook designed specifically for untargeted lipidome LC-MS data analysis, which is based on xcms software.
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26
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Lange M, Angelidou G, Ni Z, Criscuolo A, Schiller J, Blüher M, Fedorova M. AdipoAtlas: A reference lipidome for human white adipose tissue. Cell Rep Med 2021; 2:100407. [PMID: 34755127 PMCID: PMC8561168 DOI: 10.1016/j.xcrm.2021.100407] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/29/2021] [Accepted: 08/26/2021] [Indexed: 01/16/2023]
Abstract
Obesity, characterized by expansion and metabolic dysregulation of white adipose tissue (WAT), has reached pandemic proportions and acts as a primer for a wide range of metabolic disorders. Remodeling of WAT lipidome in obesity and associated comorbidities can explain disease etiology and provide valuable diagnostic and prognostic markers. To support understanding of WAT lipidome remodeling at the molecular level, we provide in-depth lipidomics profiling of human subcutaneous and visceral WAT of lean and obese individuals. We generate a human WAT reference lipidome by performing tissue-tailored preanalytical and analytical workflows, which allow accurate identification and semi-absolute quantification of 1,636 and 737 lipid molecular species, respectively. Deep lipidomic profiling allows identification of main lipid (sub)classes undergoing depot-/phenotype-specific remodeling. Previously unanticipated diversity of WAT ceramides is now uncovered. AdipoAtlas reference lipidome serves as a data-rich resource for the development of WAT-specific high-throughput methods and as a scaffold for systems medicine data integration.
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Affiliation(s)
- Mike Lange
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Georgia Angelidou
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
| | - Angela Criscuolo
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
- Thermo Fisher Scientific, Dreieich, Germany
| | - Jürgen Schiller
- Institute of Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Matthias Blüher
- Medical Department III (Endocrinology, Nephrology and Rheumatology), University of Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, Germany
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27
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Integratomics of Human Dermal Fibroblasts Treated with Low Molecular Weight Hyaluronic Acid. Molecules 2021; 26:molecules26165096. [PMID: 34443686 PMCID: PMC8399884 DOI: 10.3390/molecules26165096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
Hyaluronic acid (HA) is a glycosaminoglycan very common in commercial products from pharmaceuticals to cosmetics due to its widespread distribution in humans and its diversified physico-chemical proprieties. Despite its extended use and preliminary evidence showing even also opposite activities to the native form, the precise cellular effects of HA at low-molecular-weight (LWM-HA) are currently unclear. The ‘omics sciences currently in development offer a new and combined perspective on the cellular and organismal environment. This work aims to integrate lipidomics analyses to our previous quantitative proteomics one for a multi-omics vision of intra- and extra-cellular impact of different concentrations (0.125, 0.25, and 0.50%) of LMW-HA (20–50 kDa) on normal human dermal fibroblasts by LC-high resolution mass spectrometry (LC-HRMS). Untargeted lipidomics allowed us to identify 903 unique lipids mostly represented by triacylglycerols, ceramides, and phosphatidylcholines. According to proteomics analyses, LMW-HA 0.50% was the most effective concentration also in the lipidome rearrangement especially stimulating the synthesis of ceramides involved in skin hydration and reparation, cell signaling, and energy balance. Finally, integrative analyses showed 25 nodes covering several intra- and extra-cellular functions. The more complete comprehension of intra- and extra-cellular effects of LMW-HA here pointed out will be useful to further exploit its features and improve current formulations even though further studies on lipids biosynthesis and degradation are necessary.
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28
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Quality control requirements for the correct annotation of lipidomics data. Nat Commun 2021; 12:4771. [PMID: 34362906 PMCID: PMC8346590 DOI: 10.1038/s41467-021-24984-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/15/2021] [Indexed: 11/08/2022] Open
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29
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Vieira-Lara MA, Dommerholt MB, Zhang W, Blankestijn M, Wolters JC, Abegaz F, Gerding A, van der Veen YT, Thomas R, van Os RP, Reijngoud DJ, Jonker JW, Kruit JK, Bakker BM. Age-related susceptibility to insulin resistance arises from a combination of CPT1B decline and lipid overload. BMC Biol 2021; 19:154. [PMID: 34330275 PMCID: PMC8323306 DOI: 10.1186/s12915-021-01082-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/01/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The skeletal muscle plays a central role in glucose homeostasis through the uptake of glucose from the extracellular medium in response to insulin. A number of factors are known to disrupt the normal response to insulin leading to the emergence of insulin resistance (IR). Advanced age and a high-fat diet are factors that increase the susceptibility to IR, with lipid accumulation in the skeletal muscle being a key driver of this phenomenon. It is debated, however, whether lipid accumulation arises due to dietary lipid overload or from a decline of mitochondrial function. To gain insights into the interplay of diet and age in the flexibility of muscle lipid and glucose handling, we combined lipidomics, proteomics, mitochondrial function analysis and computational modelling to investigate young and aged mice on a low- or high-fat diet (HFD). RESULTS As expected, aged mice were more susceptible to IR when given a HFD than young mice. The HFD induced intramuscular lipid accumulation specifically in aged mice, including C18:0-containing ceramides and diacylglycerols. This was reflected by the mitochondrial β-oxidation capacity, which was upregulated by the HFD in young, but not in old mice. Conspicuously, most β-oxidation proteins were upregulated by the HFD in both groups, but carnitine palmitoyltransferase 1B (CPT1B) declined in aged animals. Computational modelling traced the flux control mostly to CPT1B, suggesting a CPT1B-driven loss of flexibility to the HFD with age. Finally, in old animals, glycolytic protein levels were reduced and less flexible to the diet. CONCLUSION We conclude that intramuscular lipid accumulation and decreased insulin sensitivity are not due to age-related mitochondrial dysfunction or nutritional overload alone, but rather to their combined effects. Moreover, we identify CPT1B as a potential target to counteract age-dependent intramuscular lipid accumulation and thereby IR.
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Affiliation(s)
- Marcel A Vieira-Lara
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
| | - Marleen B Dommerholt
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
| | - Wenxuan Zhang
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Maaike Blankestijn
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
| | - Justina C Wolters
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Fentaw Abegaz
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
| | - Albert Gerding
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
- Dutch Molecular Pathology Centre, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ydwine T van der Veen
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Rachel Thomas
- Dutch Molecular Pathology Centre, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ronald P van Os
- Central Animal Facility, Mouse Clinic for Cancer and Aging, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
| | - Johan W Jonker
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
| | - Janine K Kruit
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, Systems Medicine of Metabolism and Signaling, University Medical Center Groningen, University of Groningen, Postbus 196, 9700, AD, Groningen, The Netherlands.
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30
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Tkachev A, Stekolshchikova E, Bobrovskiy DM, Anikanov N, Ogurtsova P, Park DI, Horn AKE, Petrova D, Khrameeva E, Golub MS, Turck CW, Khaitovich P. Long-Term Fluoxetine Administration Causes Substantial Lipidome Alteration of the Juvenile Macaque Brain. Int J Mol Sci 2021; 22:ijms22158089. [PMID: 34360852 PMCID: PMC8348031 DOI: 10.3390/ijms22158089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
Fluoxetine is an antidepressant commonly prescribed not only to adults but also to children for the treatment of depression, obsessive-compulsive disorder, and neurodevelopmental disorders. The adverse effects of the long-term treatment reported in some patients, especially in younger individuals, call for a detailed investigation of molecular alterations induced by fluoxetine treatment. Two-year fluoxetine administration to juvenile macaques revealed effects on impulsivity, sleep, social interaction, and peripheral metabolites. Here, we built upon this work by assessing residual effects of fluoxetine administration on the expression of genes and abundance of lipids and polar metabolites in the prelimbic cortex of 10 treated and 11 control macaques representing two monoamine oxidase A (MAOA) genotypes. Analysis of 8871 mRNA transcripts, 3608 lipids, and 1829 polar metabolites revealed substantial alterations of the brain lipid content, including significant abundance changes of 106 lipid features, accompanied by subtle changes in gene expression. Lipid alterations in the drug-treated animals were most evident for polyunsaturated fatty acids (PUFAs). A decrease in PUFAs levels was observed in all quantified lipid classes excluding sphingolipids, which do not usually contain PUFAs, suggesting systemic changes in fatty acid metabolism. Furthermore, the residual effect of the drug on lipid abundances was more pronounced in macaques carrying the MAOA-L genotype, mirroring reported behavioral effects of the treatment. We speculate that a decrease in PUFAs may be associated with adverse effects in depressive patients and could potentially account for the variation in individual response to fluoxetine in young people.
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Affiliation(s)
- Anna Tkachev
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.T.); (E.S.); (N.A.); (P.O.); (D.P.)
| | - Elena Stekolshchikova
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.T.); (E.S.); (N.A.); (P.O.); (D.P.)
| | - Daniil M. Bobrovskiy
- Faculty of Bioengineering and Bioinformatics, Moscow State University, 119234 Moscow, Russia;
| | - Nickolay Anikanov
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.T.); (E.S.); (N.A.); (P.O.); (D.P.)
| | - Polina Ogurtsova
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.T.); (E.S.); (N.A.); (P.O.); (D.P.)
| | - Dong Ik Park
- Proteomics and Biomarkers, Max Planck Institute of Psychiatry, 80804 Munich, Germany;
| | - Anja K. E. Horn
- Institute of Anatomy and Cell Biology, Ludwig-Maximilians University, 80336 Munich, Germany;
| | - Daria Petrova
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.T.); (E.S.); (N.A.); (P.O.); (D.P.)
| | - Ekaterina Khrameeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Correspondence: (E.K.); (M.S.G.); (C.W.T.); (P.K.)
| | - Mari S. Golub
- California National Primate Research Center, University of California, Davis, CA 95616, USA
- Correspondence: (E.K.); (M.S.G.); (C.W.T.); (P.K.)
| | - Christoph W. Turck
- Proteomics and Biomarkers, Max Planck Institute of Psychiatry, 80804 Munich, Germany;
- Correspondence: (E.K.); (M.S.G.); (C.W.T.); (P.K.)
| | - Philipp Khaitovich
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.T.); (E.S.); (N.A.); (P.O.); (D.P.)
- Correspondence: (E.K.); (M.S.G.); (C.W.T.); (P.K.)
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31
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Lin WJ, Shen PC, Liu HC, Cho YC, Hsu MK, Lin IC, Chen FH, Yang JC, Ma WL, Cheng WC. LipidSig: a web-based tool for lipidomic data analysis. Nucleic Acids Res 2021; 49:W336-W345. [PMID: 34048582 PMCID: PMC8262718 DOI: 10.1093/nar/gkab419] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
With the continuing rise of lipidomic studies, there is an urgent need for a useful and comprehensive tool to facilitate lipidomic data analysis. The most important features making lipids different from general metabolites are their various characteristics, including their lipid classes, double bonds, chain lengths, etc. Based on these characteristics, lipid species can be classified into different categories and, more interestingly, exert specific biological functions in a group. In an effort to simplify lipidomic analysis workflows and enhance the exploration of lipid characteristics, we have developed a highly flexible and user-friendly web server called LipidSig. It consists of five sections, namely, Profiling, Differential Expression, Correlation, Network and Machine Learning, and evaluates lipid effects on cellular or disease phenotypes. One of the specialties of LipidSig is the conversion between lipid species and characteristics according to a user-defined characteristics table. This function allows for efficient data mining for both individual lipids and subgroups of characteristics. To expand the server's practical utility, we also provide analyses focusing on fatty acid properties and multiple characteristics. In summary, LipidSig is expected to help users identify significant lipid-related features and to advance the field of lipid biology. The LipidSig webserver is freely available at http://chenglab.cmu.edu.tw/lipidsig
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Affiliation(s)
- Wen-Jen Lin
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan
| | - Pei-Chun Shen
- Research Center for Cancer Biology, China Medical University, Taichung 40403, Taiwan
| | - Hsiu-Cheng Liu
- Research Center for Cancer Biology, China Medical University, Taichung 40403, Taiwan
| | - Yi-Chun Cho
- Research Center for Cancer Biology, China Medical University, Taichung 40403, Taiwan
| | - Min-Kung Hsu
- Research Center for Cancer Biology, China Medical University, Taichung 40403, Taiwan
| | - I-Chen Lin
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan
| | - Fang-Hsin Chen
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan 33302, Taiwan.,Department of Radiation Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan 33302, Taiwan.,Institute for Radiological Research, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan 33302, Taiwan
| | - Juan-Cheng Yang
- Chinese Medicine Research and Development Center, China Medical University Hospital, Taichung 40403, Taiwan
| | - Wen-Lung Ma
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan
| | - Wei-Chung Cheng
- Graduate Institute of Biomedical Science, China Medical University, Taichung 40403, Taiwan.,Research Center for Cancer Biology, China Medical University, Taichung 40403, Taiwan.,The Ph.D. program for Cancer Biology and Drug Discovery, China Medical University and Academia Sinica, Taichung 40403, Taiwan
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32
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Koelmel JP, Aristizabal-Henao JJ, Ni Z, Fedorova M, Kato S, Otoki Y, Nakagawa K, Lin EZ, Godri Pollitt KJ, Vasiliou V, Guingab JD, Garrett TJ, Williams TL, Bowden JA, Penumetcha M. A Novel Technique for Redox Lipidomics Using Mass Spectrometry: Application on Vegetable Oils Used to Fry Potatoes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1798-1809. [PMID: 34096708 DOI: 10.1021/jasms.1c00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Vegetables oils, rich in polyunsaturated fatty acids, are vulnerable to oxidation during manufacturing, processing, and food preparation. Currently, individual oxidation products are not well characterized, and hence, the health impacts of these unique lipid species remain unknown. Here, we introduce an extensive oxidized lipidomics in silico tandem mass spectrometry library and integrate these libraries within a user-friendly software covering a comprehensive redox lipidomics workflow. We apply this workflow to olive, soy, and walnut cooking oil; comparing unheated oil, oil after deep frying potatoes, and oil after oven frying potatoes. We annotated over a thousand oxidized triglycerides across 273 features (many coeluted). This software was validated against traditional chemical assays of oxidation, known oxidized lipids in castor oil, synthesized standards, and an alternate software LPPtiger. Development of these new software programs for redox lipidomics opens the door to characterize health implications of individual oxidation products.
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Affiliation(s)
- Jeremy P Koelmel
- School of Public Health, Yale University, New Haven, Connecticut, 06520, United States
| | - Juan J Aristizabal-Henao
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida 32608, United States
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig 01403Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, 04103, Germany
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Leipzig 01403Germany
- Center for Biotechnology and Biomedicine, University of Leipzig, Leipzig, 04103, Germany
| | - Shunji Kato
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8577, Japan
| | - Yurika Otoki
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8577, Japan
| | - Kiyotaka Nakagawa
- Food and Biodynamic Chemistry Laboratory, Graduate School of Agricultural Science, Tohoku University, Sendai 980-8577, Japan
| | - Elizabeth Z Lin
- School of Public Health, Yale University, New Haven, Connecticut, 06520, United States
| | | | - Vasilis Vasiliou
- School of Public Health, Yale University, New Haven, Connecticut, 06520, United States
| | - Joy D Guingab
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, United States
- Department of Chemistry, University of Florida, Gainesville, Florida 32610, United States
| | - Traycie L Williams
- School of Nutrition, Kinesiology and Psychological Science, University of Central Missouri, Warrensburg, Missouri 64093, United States
| | - John A Bowden
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, Florida 32608, United States
- Department of Chemistry, University of Florida, Gainesville, Florida 32610, United States
| | - Meera Penumetcha
- School of Nutrition, Kinesiology and Psychological Science, University of Central Missouri, Warrensburg, Missouri 64093, United States
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33
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Kyle JE, Aimo L, Bridge AJ, Clair G, Fedorova M, Helms JB, Molenaar MR, Ni Z, Orešič M, Slenter D, Willighagen E, Webb-Robertson BJM. Interpreting the lipidome: bioinformatic approaches to embrace the complexity. Metabolomics 2021; 17:55. [PMID: 34091802 DOI: 10.1007/s11306-021-01802-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/18/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Improvements in mass spectrometry (MS) technologies coupled with bioinformatics developments have allowed considerable advancement in the measurement and interpretation of lipidomics data in recent years. Since research areas employing lipidomics are rapidly increasing, there is a great need for bioinformatic tools that capture and utilize the complexity of the data. Currently, the diversity and complexity within the lipidome is often concealed by summing over or averaging individual lipids up to (sub)class-based descriptors, losing valuable information about biological function and interactions with other distinct lipids molecules, proteins and/or metabolites. AIM OF REVIEW To address this gap in knowledge, novel bioinformatics methods are needed to improve identification, quantification, integration and interpretation of lipidomics data. The purpose of this mini-review is to summarize exemplary methods to explore the complexity of the lipidome. KEY SCIENTIFIC CONCEPTS OF REVIEW Here we describe six approaches that capture three core focus areas for lipidomics: (1) lipidome annotation including a resolvable database identifier, (2) interpretation via pathway- and enrichment-based methods, and (3) understanding complex interactions to emphasize specific steps in the analytical process and highlight challenges in analyses associated with the complexity of lipidome data.
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Affiliation(s)
- Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Lucila Aimo
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211, Geneva 4, Switzerland
| | - Alan J Bridge
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211, Geneva 4, Switzerland
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany
| | - J Bernd Helms
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Martijn R Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, Leipzig, Germany
| | - Matej Orešič
- School of Medical Sciences, Örebro University, 702 81, Örebro, Sweden
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Denise Slenter
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, 6229 ER, Maastricht, The Netherlands
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, 6229 ER, Maastricht, The Netherlands
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34
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Kösters M, Leufken J, Leidel SA. SMITER-A Python Library for the Simulation of LC-MS/MS Experiments. Genes (Basel) 2021; 12:396. [PMID: 33799543 PMCID: PMC8000309 DOI: 10.3390/genes12030396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 12/24/2022] Open
Abstract
SMITER (Synthetic mzML writer) is a Python-based command-line tool designed to simulate liquid-chromatography-coupled tandem mass spectrometry LC-MS/MS runs. It enables the simulation of any biomolecule amenable to mass spectrometry (MS) since all calculations are based on chemical formulas. SMITER features a modular design, allowing for an easy implementation of different noise and fragmentation models. By default, SMITER uses an established noise model and offers several methods for peptide fragmentation, and two models for nucleoside fragmentation and one for lipid fragmentation. Due to the rich Python ecosystem, other modules, e.g., for retention time (RT) prediction, can easily be implemented for the tailored simulation of any molecule of choice. This facilitates the generation of defined gold-standard LC-MS/MS datasets for any type of experiment. Such gold standards, where the ground truth is known, are required in computational mass spectrometry to test new algorithms and to improve parameters of existing ones. Similarly, gold-standard datasets can be used to evaluate analytical challenges, e.g., by predicting co-elution and co-fragmentation of molecules. As these challenges hinder the detection or quantification of co-eluents, a comprehensive simulation can identify and thus, prevent such difficulties before performing actual MS experiments. SMITER allows the creation of such datasets easily, fast, and efficiently.
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Affiliation(s)
| | | | - Sebastian A. Leidel
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP), University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (M.K.); (J.L.)
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35
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Gaud C, C Sousa B, Nguyen A, Fedorova M, Ni Z, O'Donnell VB, Wakelam MJO, Andrews S, Lopez-Clavijo AF. BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS. F1000Res 2021; 10:4. [PMID: 33564392 PMCID: PMC7848852 DOI: 10.12688/f1000research.28022.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
Abstract
Lipidomics increasingly describes the quantification using mass spectrometry of all lipids present in a biological sample. As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment. Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways. As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging. BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways. BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.
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Affiliation(s)
- Caroline Gaud
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Bebiana C Sousa
- Lipidomics facility, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - An Nguyen
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, 04109, Germany
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, 04109, Germany
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Michael J O Wakelam
- Lipidomics facility, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Andrea F Lopez-Clavijo
- Lipidomics facility, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
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36
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Gaud C, C. Sousa B, Nguyen A, Fedorova M, Ni Z, O’Donnell VB, Wakelam MJ, Andrews S, Lopez-Clavijo AF. BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS. F1000Res 2021; 10:4. [PMID: 33564392 PMCID: PMC7848852 DOI: 10.12688/f1000research.28022.1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 08/13/2023] Open
Abstract
Lipidomics increasingly describes the quantification using mass spectrometry of all lipids present in a biological sample. As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment. Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways. As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging. BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways. BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.
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Affiliation(s)
- Caroline Gaud
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Bebiana C. Sousa
- Lipidomics facility, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - An Nguyen
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, 04109, Germany
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, 04109, Germany
| | - Valerie B. O’Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Michael J.O. Wakelam
- Lipidomics facility, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
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37
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Hartler J, Armando AM, Trötzmüller M, Dennis EA, Köfeler HC, Quehenberger O. Automated Annotation of Sphingolipids Including Accurate Identification of Hydroxylation Sites Using MS n Data. Anal Chem 2020; 92:14054-14062. [PMID: 33003696 PMCID: PMC7581017 DOI: 10.1021/acs.analchem.0c03016] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sphingolipids constitute a heterogeneous lipid category that is involved in many key cellular functions. For high-throughput analyses of sphingolipids, tandem mass spectrometry (MS/MS) is the method of choice, offering sufficient sensitivity, structural information, and quantitative precision for detecting hundreds to thousands of species simultaneously. While glycerolipids and phospholipids are predominantly non-hydroxylated, sphingolipids are typically dihydroxylated. However, species containing one or three hydroxylation sites can be detected frequently. This variability in the number of hydroxylation sites on the sphingolipid long-chain base and the fatty acyl moiety produces many more isobaric species and fragments than for other lipid categories. Due to this complexity, the automated annotation of sphingolipid species is challenging, and incorrect annotations are common. In this study, we present an extension of the Lipid Data Analyzer (LDA) "decision rule set" concept that considers the structural characteristics that are specific for this lipid category. To address the challenges inherent to automated annotation of sphingolipid structures from MS/MS data, we first developed decision rule sets using spectra from authentic standards and then tested the applicability on biological samples including murine brain and human plasma. A benchmark test based on the murine brain samples revealed a highly improved annotation quality as measured by sensitivity and reliability. The results of this benchmark test combined with the easy extensibility of the software to other (sphingo)lipid classes and the capability to detect and correctly annotate novel sphingolipid species make LDA broadly applicable to automated sphingolipid analysis, especially in high-throughput settings.
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Affiliation(s)
- Jürgen Hartler
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States.,Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1/I, 8010 Graz, Austria
| | - Aaron M Armando
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstraße 24, 8010 Graz, Austria
| | - Edward A Dennis
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstraße 24, 8010 Graz, Austria
| | - Oswald Quehenberger
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
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38
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Abstract
We present Mass Spectrometry-Data Independent Analysis software version 4 (MS-DIAL 4), a comprehensive lipidome atlas with retention time, collision cross-section and tandem mass spectrometry information. We formulated mass spectral fragmentations of lipids across 117 lipid subclasses and included ion mobility tandem mass spectrometry. Using human, murine, algal and plant biological samples, we annotated and semiquantified 8,051 lipids using MS-DIAL 4 with a 1-2% estimated false discovery rate. MS-DIAL 4 helps standardize lipidomics data and discover lipid pathways.
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39
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Criscuolo A, Zeller M, Fedorova M. Evaluation of Lipid In-Source Fragmentation on Different Orbitrap-based Mass Spectrometers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:463-466. [PMID: 32031403 DOI: 10.1021/jasms.9b00061] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Natural lipidomes represent a complex mixture of lipid molecular species with a variety of biological and signaling functions. Modern mass spectrometry (MS)-based analytical platforms are often used to resolve the complexity of natural lipidomes. The quantitative transfer of lipid molecular species in the gas phase during the electrospray ionization required for MS analysis might be challenged by lipid in-source fragmentation (ISF) hampering their accurate identification and quantification. Here we evaluated the effect of transmission radio frequency (RF) levels and ion transfer temperatures (ITTs) on the analysis of four different lipids (ceramide, cholesteryl ester, phosphatidylethanolamine, and triacylglyceride) ionized in positive ion mode on three different Orbitrap-based platforms. ITT and RF levels were ramped in a systematic way to determine the best settings, allowing the most sensitive detection accompanied by the lowest ISF of a lipid. The extent of the ISF was shown to depend on the configurations of the transmission devices (S-lens vs letterbox/ion funnel) at defined RF and ITT levels for each studied lipid class. We provide here the recommendations for reducing the extent of lipid ISF without a significant loss in sensitivity for Q Exactive HF, Q Exactive HF-X, and Orbitrap Fusion Lumos platforms.
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Affiliation(s)
- Angela Criscuolo
- Thermo Fisher Scientific , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy , Universität Leipzig , Deutscher Platz 5 , 04103 Leipzig , Germany
- Center for Biotechnology and Biomedicine , Universität Leipzig , Deutscher Platz 5 , 04103 Leipzig , Germany
| | - Martin Zeller
- Thermo Fisher Scientific , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy , Universität Leipzig , Deutscher Platz 5 , 04103 Leipzig , Germany
- Center for Biotechnology and Biomedicine , Universität Leipzig , Deutscher Platz 5 , 04103 Leipzig , Germany
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40
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Helmer PO, Korf A, Hayen H. Analysis of artificially oxidized cardiolipins and monolyso-cardiolipins via liquid chromatography/high-resolution mass spectrometry and Kendrick mass defect plots after hydrophilic interaction liquid chromatography based sample preparation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8566. [PMID: 31469924 DOI: 10.1002/rcm.8566] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/21/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Cardiolipins (CL) are a special lipid class which plays a main role in energy metabolism in mitochondria and is involved in apoptosis. In contrast to other glycerophospholipids, they contain four fatty acyl residues which results in a high structural diversity. Oxidation, for example by reactive oxygen species, or lyso forms such as monolyso-CL (MLCL), increases this diversity. Mass spectrometric analysis and computational identification of CL, MLCL and their oxidation products is therefore a challenging task. METHODS In order to distinguish CL, MLCL and their oxidation products, a liquid chromatography/tandem mass spectrometry (LC/MS/MS) method was developed. A hydrophilic interaction liquid chromatography (HILIC)-based solid-phase extraction (SPE) clean-up approach was developed for CL enrichment. Graphical analysis of CL, MLCL and their oxidation products was carried out by a three-dimensional Kendrick mass defect (3D-KMD) plot module, as well as a refined lipid search module of the open-source metabolomics data mining software MZmine 2. RESULTS The HILIC-based SPE clean-up enabled complete separation of polar and nonpolar lipid classes. A yeast (Saccharomyces cerevisiae) lipid extract, which was artificially oxidized by means of the Fenton reaction, was analyzed by the developed LC/MS/MS method. CL species with differences in chain length and degree of unsaturation have been separated by high-performance liquid chromatography (HPLC). In total 66 CL, MLCL and oxidized species have been identified utilizing 3D-KMD plots in combination with database matching using MZmine 2. For further characterization of annotated species, MS/MS experiments have been utilized. CONCLUSIONS 3D-KMD plots capturing chromatographic and high-resolution mass spectrometry data have been successfully used for graphical identification of CL, MLCL as well as their oxidized species. Therefore, we chose multiple KMD bases such as hydrogen and oxygen to visualize the degree of unsaturation and oxidation capturing chromatographic data by means of a color-coded paint scale as the third dimension. In combination with database matching, the analysis of low concentrated lipid species in complex samples has been significantly improved.
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Affiliation(s)
- Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Ansgar Korf
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149, Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, 48149, Münster, Germany
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41
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Ni Z, Goracci L, Cruciani G, Fedorova M. Computational solutions in redox lipidomics - Current strategies and future perspectives. Free Radic Biol Med 2019; 144:110-123. [PMID: 31035005 DOI: 10.1016/j.freeradbiomed.2019.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/15/2019] [Accepted: 04/23/2019] [Indexed: 12/31/2022]
Abstract
The high chemical diversity of lipids allows them to perform multiple biological functions ranging from serving as structural building blocks of biological membranes to regulation of metabolism and signal transduction. In addition to the native lipidome, lipid species derived from enzymatic and non-enzymatic modifications (the epilipidome) make the overall picture even more complex, as their functions are still largely unknown. Oxidized lipids represent the fraction of epilipidome which has attracted high scientific attention due to their apparent involvement in the onset and development of numerous human disorders. Development of high-throughput analytical methods such as liquid chromatography coupled on-line to mass spectrometry provides the possibility to address epilipidome diversity in complex biological samples. However, the main bottleneck of redox lipidomics, the branch of lipidomics dealing with the characterization of oxidized lipids, remains the lack of optimal computational tools for robust, accurate and specific identification of already discovered and yet unknown modified lipids. Here we discuss the main principles of high-throughput identification of lipids and their modified forms and review the main software tools currently available in redox lipidomics. Different levels of confidence for software assisted identification of redox lipidome are defined and necessary steps toward optimal computational solutions are proposed.
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Affiliation(s)
- Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, Leipzig, Germany
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy; Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123 Perugia, Italy; Consortium for Computational Molecular and Materials Sciences (CMS), via Elce di Sotto 8, 06123 Perugia, Italy
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, Leipzig, Germany.
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42
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Criscuolo A, Zeller M, Cook K, Angelidou G, Fedorova M. Rational selection of reverse phase columns for high throughput LC–MS lipidomics. Chem Phys Lipids 2019; 221:120-127. [DOI: 10.1016/j.chemphyslip.2019.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/07/2019] [Accepted: 03/14/2019] [Indexed: 12/17/2022]
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Striesow J, Lackmann JW, Ni Z, Wenske S, Weltmann KD, Fedorova M, von Woedtke T, Wende K. Oxidative modification of skin lipids by cold atmospheric plasma (CAP): A standardizable approach using RP-LC/MS 2 and DI-ESI/MS 2. Chem Phys Lipids 2019; 226:104786. [PMID: 31229410 DOI: 10.1016/j.chemphyslip.2019.104786] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022]
Abstract
Cold atmospheric plasma (CAP) is an emerging source for the locally defined delivery of reactive species, and its clinical potential has been identified in the control of inflammatory processes, such as acute and chronic wounds, or cancerous lesions. Lipids, due to their localization and chemical structure as ideal targets for oxidative species, are relevant modifiers of physiological processes. Human forehead lipids collected on a target were treated by an argon plasma jet and immediately analyzed by direct-infusion high-resolution tandem mass spectrometry (DI-MS2) or liquid chromatography-tandem MS (RP-LC/MS2). Subsequent data analysis was performed by LipidHunter (University of Leipzig), LipidXplorer (Max Planck Institute of Molecular Cell Biology and Genetics, Dresden), and LipidSearch (Thermo Scientific). With either MS method, all major lipid classes of sebum lipids were detected. Significant differences regarding triacylglycerols (predominantly identified in RP-LC/MS2) and ceramides (predominantly identified in DI-MS2) indicate experimental- or approach-inherent distinctions. A CAP-driven oxidation of triacyclglycerols, ceramides, and cholesteryl esters was detected such as truncations and hydroperoxylations, but at a significantly lower extent than expected. Scavenging of reactive species due to naturally present antioxidants in the samples and the absence of a liquid interphase to allow reactive species deposition by the CAP will have contributed to the limited amount of oxidation products observed. In addition, limitations of the software's capability of identifying unexpected oxidized lipids potentially led to an underestimation of the CAP impact on skin lipids, indicating a need for further software development. With respect to the clinical application of CAP, the result indicates that intact skin with its sebum/epidermal lipid overlay is well protected and that moderate treatment will yield limited (if any) functional consequences in the dermal tissue.
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Affiliation(s)
- Johanna Striesow
- ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology (INP Greifswald), Felix-Hausdorff-Straße 2, 17489 Greifswald, Germany
| | - Jan-Wilm Lackmann
- ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology (INP Greifswald), Felix-Hausdorff-Straße 2, 17489 Greifswald, Germany
| | - Zhixu Ni
- Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany
| | - Sebastian Wenske
- ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology (INP Greifswald), Felix-Hausdorff-Straße 2, 17489 Greifswald, Germany
| | - Klaus-Dieter Weltmann
- Leibniz Institute for Plasma Science and Technology (INP Greifswald), Felix-Hausdorff-Straße 2, 17489 Greifswald, Germany
| | - Maria Fedorova
- Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany; Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany
| | - Thomas von Woedtke
- Leibniz Institute for Plasma Science and Technology (INP Greifswald), Felix-Hausdorff-Straße 2, 17489 Greifswald, Germany; Greifswald University Medicine, Fleischmannstraße 8, 17475 Greifswald, Germany
| | - Kristian Wende
- ZIK Plasmatis, Leibniz Institute for Plasma Science and Technology (INP Greifswald), Felix-Hausdorff-Straße 2, 17489 Greifswald, Germany.
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Korf A, Jeck V, Schmid R, Helmer PO, Hayen H. Lipid Species Annotation at Double Bond Position Level with Custom Databases by Extension of the MZmine 2 Open-Source Software Package. Anal Chem 2019; 91:5098-5105. [PMID: 30892876 DOI: 10.1021/acs.analchem.8b05493] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In recent years, proprietary and open-source bioinformatics software tools have been developed for the identification of lipids in complex biological samples based on high-resolution mass spectrometry data. These existent software tools often rely on publicly available lipid databases, such as LIPID MAPS, which, in some cases, only contain a limited number of lipid species for a specific lipid class. Other software solutions implement their own lipid species databases, which are often confined regarding implemented lipid classes, such as phospholipids. To address these drawbacks, we provide an extension of the widely used open-source metabolomics software MZmine 2, which enables the annotation of detected chromatographic features as lipid species. The extension is designed for straightforward generation of a custom database for selected lipid classes. Furthermore, each lipid's sum formula of the created database can be rapidly modified to search for derivatization products, oxidation products, in-source fragments, or adducts. The versatility will be exemplified by a liquid chromatography-high resolution mass spectrometry data set with postcolumn Paternò-Büchi derivatization. The derivatization reaction was performed to pinpoint the double bond positions in diacylglyceryltrimethylhomoserine lipid species in a lipid extract of a green algae ( Chlamydomonas reinhardtii) sample. The developed Lipid Search module extension of MZmine 2 supports the identification of lipids as far as double bond position level.
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Affiliation(s)
- Ansgar Korf
- Institute of Inorganic and Analytical Chemistry , University of Münster , Corrensstraße 30 , 48149 Münster , Germany
| | - Viola Jeck
- Institute of Inorganic and Analytical Chemistry , University of Münster , Corrensstraße 30 , 48149 Münster , Germany
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry , University of Münster , Corrensstraße 30 , 48149 Münster , Germany
| | - Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry , University of Münster , Corrensstraße 30 , 48149 Münster , Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry , University of Münster , Corrensstraße 30 , 48149 Münster , Germany
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Narzt MS, Nagelreiter IM, Oskolkova O, Bochkov VN, Latreille J, Fedorova M, Ni Z, Sialana FJ, Lubec G, Filzwieser M, Laggner M, Bilban M, Mildner M, Tschachler E, Grillari J, Gruber F. A novel role for NUPR1 in the keratinocyte stress response to UV oxidized phospholipids. Redox Biol 2018; 20:467-482. [PMID: 30466060 PMCID: PMC6243031 DOI: 10.1016/j.redox.2018.11.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/30/2018] [Accepted: 11/08/2018] [Indexed: 02/08/2023] Open
Abstract
Ultraviolet light is the dominant environmental oxidative skin stressor and a major skin aging factor. We studied which oxidized phospholipid (OxPL) mediators would be generated in primary human keratinocytes (KC) upon exposure to ultraviolet A light (UVA) and investigated the contribution of OxPL to UVA responses. Mass spectrometric analysis immediately or 24 h post UV stress revealed significant changes in abundance of 173 and 84 lipid species, respectively. We identified known and novel lipid species including known bioactive and also potentially reactive carbonyl containing species. We found indication for selective metabolism and degradation of selected reactive lipids. Exposure to both UVA and to in vitro UVA - oxidized phospholipids activated, on transcriptome and proteome level, NRF2/antioxidant response signaling, lipid metabolizing enzyme expression and unfolded protein response (UPR) signaling. We identified NUPR1 as an upstream regulator of UVA/OxPL transcriptional stress responses and found this protein to be expressed in the epidermis. Silencing of NUPR1 resulted in augmented expression of antioxidant and lipid detoxification genes and disturbed the cell cycle, making it a potential key factor in skin reactive oxygen species (ROS) responses intimately involved in aging and pathology.
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Affiliation(s)
- Marie-Sophie Narzt
- Department of Dermatology, Medical University of Vienna, Vienna, Austria; Christian Doppler Laboratory for Biotechnology of Skin Aging, Austria
| | - Ionela-Mariana Nagelreiter
- Department of Dermatology, Medical University of Vienna, Vienna, Austria; Christian Doppler Laboratory for Biotechnology of Skin Aging, Austria
| | - Olga Oskolkova
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
| | - Valery N Bochkov
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
| | - Julie Latreille
- Department of Biology & Women's Beauty, Chanel, Pantin, France
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry, Universität Leipzig, Leipzig, Germany; Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
| | - Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry, Universität Leipzig, Leipzig, Germany; Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
| | - Fernando J Sialana
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Gert Lubec
- Paracelsus Medical University of Salzburg, Salzburg, Austria
| | - Manuel Filzwieser
- Christian Doppler Laboratory for Biotechnology of Skin Aging, Austria
| | - Maria Laggner
- Department of Ophthalmology and Optometry, Medical University of Vienna, Vienna, Austria
| | - Martin Bilban
- Department of Laboratory Medicine & Core Facility Genomics, Medical University of Vienna, Vienna, Austria
| | - Michael Mildner
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Erwin Tschachler
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Johannes Grillari
- Christian Doppler Laboratory for Biotechnology of Skin Aging, Austria; Department of Biotechnology, BOKU, University of Natural Resources and Life Sciences Vienna, Austria
| | - Florian Gruber
- Department of Dermatology, Medical University of Vienna, Vienna, Austria; Christian Doppler Laboratory for Biotechnology of Skin Aging, Austria.
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46
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Misra BB. New tools and resources in metabolomics: 2016-2017. Electrophoresis 2018; 39:909-923. [PMID: 29292835 DOI: 10.1002/elps.201700441] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 12/17/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
Rapid advances in mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based platforms for metabolomics have led to an upsurge of data every single year. Newer high-throughput platforms, hyphenated technologies, miniaturization, and tool kits in data acquisition efforts in metabolomics have led to additional challenges in metabolomics data pre-processing, analysis, interpretation, and integration. Thanks to the informatics, statistics, and computational community, new resources continue to develop for metabolomics researchers. The purpose of this review is to provide a summary of the metabolomics tools, software, and databases that were developed or improved during 2016-2017, thus, enabling readers, developers, and researchers access to a succinct but thorough list of resources for further improvisation, implementation, and application in due course of time.
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Affiliation(s)
- Biswapriya B Misra
- Department of Internal Medicine, Section of Molecular Medicine, Medical Center Boulevard, Winston-Salem, NC, USA
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Ni Z, Angelidou G, Hoffmann R, Fedorova M. LPPtiger software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets. Sci Rep 2017; 7:15138. [PMID: 29123162 PMCID: PMC5680299 DOI: 10.1038/s41598-017-15363-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/25/2017] [Indexed: 12/03/2022] Open
Abstract
Oxidized phospholipids (oxPLs) have been recently recognized as important mediators of various and often controversial cellular functions and stress responses. Due to the low concentrations in vivo, oxPL detection is mostly performed by targeted mass spectrometry. Although significantly improving the sensitivity, this approach does not provide a comprehensive view on oxPLs required for understanding oxPL functional activities. While capable of providing information on the diversity of oxPLs, the main challenge of untargeted lipidomics is the absence of bioinformatics tools to support high-throughput identification of previously unconsidered, oxidized lipids. Here, we present LPPtiger, an open-source software tool for oxPL identification from data-dependent LC-MS datasets. LPPtiger combines three unique algorithms to predict oxidized lipidome, generate oxPL spectra libraries, and identify oxPLs from tandem MS data using parallel processing and a multi-scoring identification workflow.
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Affiliation(s)
- Zhixu Ni
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Georgia Angelidou
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Ralf Hoffmann
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany.,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany. .,Center for Biotechnology and Biomedicine, Universität Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany.
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