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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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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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Liakh I, Pakiet A, Sledzinski T, Mika A. Methods of the Analysis of Oxylipins in Biological Samples. Molecules 2020; 25:E349. [PMID: 31952163 PMCID: PMC7024226 DOI: 10.3390/molecules25020349] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/11/2022] Open
Abstract
Oxylipins are derivatives of polyunsaturated fatty acids and due to their important and diverse functions in the body, they have become a popular subject of studies. The main challenge for researchers is their low stability and often very low concentration in samples. Therefore, in recent years there have been developments in the extraction and analysis methods of oxylipins. New approaches in extraction methods were described in our previous review. In turn, the old analysis methods have been replaced by new approaches based on mass spectrometry (MS) coupled with liquid chromatography (LC) and gas chromatography (GC), and the best of these methods allow hundreds of oxylipins to be quantitatively identified. This review presents comparative and comprehensive information on the progress of various methods used by various authors to achieve the best results in the analysis of oxylipins in biological samples.
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Affiliation(s)
- Ivan Liakh
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Debinki 1, 80-211 Gdansk, Poland; (I.L.); (T.S.)
| | - Alicja Pakiet
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Debinki 1, 80-211 Gdansk, Poland; (I.L.); (T.S.)
| | - Adriana Mika
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Debinki 1, 80-211 Gdansk, Poland; (I.L.); (T.S.)
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland;
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Wang J, Wang C, Han X. Tutorial on lipidomics. Anal Chim Acta 2019; 1061:28-41. [PMID: 30926037 PMCID: PMC7375172 DOI: 10.1016/j.aca.2019.01.043] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 01/16/2019] [Accepted: 01/18/2019] [Indexed: 12/20/2022]
Abstract
The mainstream of lipidomics involves mass spectrometry-based, systematic, and large-scale studies of the structure, composition, and quantity of lipids in biological systems such as organs, cells, and body fluids. As increasingly more researchers in broad fields are beginning to pay attention to and actively learn about the lipidomic technology, some introduction on the topic is needed to help the newcomers to better understand the field. This tutorial seeks to introduce the basic knowledge about lipidomics and to provide readers with some core ideas and the most important approaches for studying the field.
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Affiliation(s)
- Jianing Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Chunyan Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA; Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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Vu N, Narvaez-Rivas M, Chen GY, Rewers MJ, Zhang Q. Accurate mass and retention time library of serum lipids for type 1 diabetes research. Anal Bioanal Chem 2019; 411:5937-5949. [PMID: 31280478 DOI: 10.1007/s00216-019-01997-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022]
Abstract
Dysregulated lipid species are linked to various disease pathologies and implicated as potential biomarkers for type 1 diabetes (T1D). However, it is challenging to comprehensively profile the blood specimen lipidome with full structural details of every lipid molecule. The commonly used reversed-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS)-based lipidomics approach is powerful for the separation of individual lipid species, but lipids belonging to different classes may still co-elute and result in ion suppression and misidentification of lipids. Using offline mixed-mode and RPLC-based two-dimensional separations coupled with MS/MS, a comprehensive lipidomic profiling was performed on human sera pooled from healthy and T1D subjects. The elution order of lipid molecular species on RPLC showed good correlations to the total number of carbons in fatty acyl chains and total number of double bonds. This observation together with fatty acyl methyl ester analysis was used to enhance the confidence of identified lipid species. The final T1D serum lipid library database contains 753 lipid molecular species with accurate mass and RPLC retention time uniquely annotated for each of the species. This comprehensive human serum lipid library can serve as a database for high-throughput RPLC-MS-based lipidomic analysis of blood samples related to T1D and other childhood diseases. Graphical abstract.
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Affiliation(s)
- Ngoc Vu
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27412, USA.,Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28082, USA
| | - Monica Narvaez-Rivas
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28082, USA
| | - Guan-Yuan Chen
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28082, USA
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Qibin Zhang
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, 27412, USA. .,Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC, 28082, USA.
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