1
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Ventura G, Bianco M, Calvano CD, Bianco G, Di Capua A, Coniglio D, Losito I, Cataldi TRI. Mass spectrometric characterization of aminophospholipids containing N-(2-hydroxyethyl)glycine in kombu algae extracts. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9843. [PMID: 38924168 DOI: 10.1002/rcm.9843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024]
Abstract
RATIONALE 1,2-Diacyl-sn-glycero-3-phospho-O-[N-(2-hydroxyethyl)glycines] (PHEGs) are a class of rare aminophospholipids found specifically in brown algae, including kombu seaweed. Despite their potential importance in algal physiology, a comprehensive mass spectrometry (MS) characterization, useful to understand their biological behaviour, is still lacking. METHODS To establish the structural regiochemical features of PHEGs, we employed hydrophilic interaction liquid chromatography (HILIC). Following separation, the isolated band of PHEGs was analyzed using MS techniques. This included multistage tandem MS experiments, performed in both positive and negative electrospray ionization modes at low and high resolution. RESULTS By comparing MS/MS and MS3 spectra acquired in negative ion mode, the regiochemical rules for PHEG identification were established. The most abundant PHEG species in kombu seaweed, from both Laminaria ochroleuca (European Atlantic) and Laminaria longissima (Japan), was identified as PHEG 20:4/20:4. Less abundant species included PHEG 20:4/20:5 and hydroxylated forms of both PHEG 20:4/20:4 (i.e. 40:8;O) and 20:4/20:5 (40:9;O). The presence of a lyso PHEG 20:4 was consistently detected but at very low levels. CONCLUSIONS This study employed MS analysis to elucidate the regiochemical patterns of PHEGs in kombu seaweed. We identified PHEG 20:4/20:4 as the dominant species, along with several less abundant variants, including hydroxylated forms. These findings provide valuable insights into the potential roles and metabolism of PHEGs in brown algae, paving the way for further investigation into their biological functions.
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Affiliation(s)
- Giovanni Ventura
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
| | | | - Cosima Damiana Calvano
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
| | - Giuliana Bianco
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
| | - Angela Di Capua
- Dipartimento di Scienze, Università degli Studi della Basilicata, Potenza, Italy
| | - Davide Coniglio
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
| | - Ilario Losito
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
| | - Tommaso R I Cataldi
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
- Interdepartmental Research Center SMART, University of Bari Aldo Moro, Bari, Italy
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2
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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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3
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Heuckeroth S, Damiani T, Smirnov A, Mokshyna O, Brungs C, Korf A, Smith JD, Stincone P, Dreolin N, Nothias LF, Hyötyläinen T, Orešič M, Karst U, Dorrestein PC, Petras D, Du X, van der Hooft JJJ, Schmid R, Pluskal T. Reproducible mass spectrometry data processing and compound annotation in MZmine 3. Nat Protoc 2024:10.1038/s41596-024-00996-y. [PMID: 38769143 DOI: 10.1038/s41596-024-00996-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/26/2024] [Indexed: 05/22/2024]
Abstract
Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is an open-source software for the processing of raw spectral data generated by different MS platforms. Examples include liquid chromatography-MS, gas chromatography-MS and MS-imaging. These data might typically be associated with various applications including metabolomics and lipidomics. Moreover, the third version of the software, described herein, supports the processing of ion mobility spectrometry (IMS) data. The present protocol provides three distinct procedures to perform feature detection and annotation of untargeted MS data produced by different instrumental setups: liquid chromatography-(IMS-)MS, gas chromatography-MS and (IMS-)MS imaging. For training purposes, example datasets are provided together with configuration batch files (i.e., list of processing steps and parameters) to allow new users to easily replicate the described workflows. Depending on the number of data files and available computing resources, we anticipate this to take between 2 and 24 h for new MZmine users and nonexperts. Within each procedure, we provide a detailed description for all processing parameters together with instructions/recommendations for their optimization. The main generated outputs are represented by aligned feature tables and fragmentation spectra lists that can be used by other third-party tools for further downstream analysis.
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Affiliation(s)
| | - Tito Damiani
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Olena Mokshyna
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Corinna Brungs
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ansgar Korf
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Joshua David Smith
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
- First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | | | - Louis-Félix Nothias
- University of Geneva, Geneva, Switzerland
- Université Côte d'Azur, CNRS, ICN, Nice, France
| | | | - Matej Orešič
- Örebro University, Örebro, Sweden
- University of Turku and Åbo Akademi University, Turku, Finland
| | - Uwe Karst
- University of Münster, Münster, Germany
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- University of Tuebingen, Tuebingen, Germany
- University of California Riverside, Riverside, CA, USA
| | - Xiuxia Du
- University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Justin J J van der Hooft
- Wageningen University & Research, Wageningen, the Netherlands
- University of Johannesburg, Johannesburg, South Africa
| | - Robin Schmid
- University of Münster, Münster, Germany.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Tomáš Pluskal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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4
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Bessler S, Soltwisch J, Dreisewerd K. Visualization of Differential Cardiolipin Profiles in Murine Retinal Cell Layers by High-Resolution MALDI Mass Spectrometry Imaging. Anal Chem 2023; 95:11352-11358. [PMID: 37458700 DOI: 10.1021/acs.analchem.3c01465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
The precise fatty acyl chain configuration of cardiolipin (CL), a tetrameric mitochondrial-specific membrane lipid, exhibits dependence on cell and tissue types. A powerful method to map CL profiles in tissue sections in a spatially resolved manner is matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). To build on and explore this potential, we employed a quadrupole time-of-flight mass spectrometer along with optimized sample preparation protocols. We imaged the CL profiles of individual murine retinal cell layers at a pixel size of 10 μm. In combination with tandem MS, we obtained detailed insights into the CL composition of individual retinal cell layers. In particular, we found differential expression of the polyunsaturated fatty acids (PUFA) linoleic, arachidonic, and docosahexaenoic acids. PUFAs are prone to peroxidation and hence regarded as critical factors in development and progression of retinal pathologies, such as age-related macular degeneration (AMD). The ability of MALDI-MSI to provide cues on the CL composition in neuronal tissue with close to single-cell resolution can provide important insights into retinal physiology in health and disease.
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Affiliation(s)
- Sebastian Bessler
- Institute of Hygiene, University of Münster, Robert-Koch-Str. 41, 48149 Münster, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, Robert-Koch-Str. 41, 48149 Münster, Germany
| | - Klaus Dreisewerd
- Institute of Hygiene, University of Münster, Robert-Koch-Str. 41, 48149 Münster, Germany
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5
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Damiani T, Bonciarelli S, Thallinger GG, Koehler N, Krettler CA, Salihoğlu AK, Korf A, Pauling JK, Pluskal T, Ni Z, Goracci L. Software and Computational Tools for LC-MS-Based Epilipidomics: Challenges and Solutions. Anal Chem 2023; 95:287-303. [PMID: 36625108 PMCID: PMC9835057 DOI: 10.1021/acs.analchem.2c04406] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Tito Damiani
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Praha 6, Czech Republic
| | - Stefano Bonciarelli
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | - Gerhard G. Thallinger
- Institute
of Biomedical Informatics, Graz University
of Technology, 8010 Graz, Austria,
| | - Nikolai Koehler
- LipiTUM,
Chair of Experimental Bioinformatics, Technical
University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | | | - Arif K. Salihoğlu
- Department
of Physiology, Faculty of Medicine and Institute of Health Sciences, Karadeniz Technical University, 61080 Trabzon, Turkey
| | - Ansgar Korf
- Bruker Daltonics
GmbH & Co. KG, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Josch K. Pauling
- LipiTUM,
Chair of Experimental Bioinformatics, Technical
University of Munich, Maximus-von-Imhof Forum 3, 85354 Freising, Germany
| | - Tomáš Pluskal
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 160 00 Praha 6, Czech Republic
| | - Zhixu Ni
- Center of
Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy,
| | - Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy,
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6
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Bautista JS, Falabella M, Flannery PJ, Hanna MG, Heales SJ, Pope SA, Pitceathly RD. Advances in methods to analyse cardiolipin and their clinical applications. Trends Analyt Chem 2022; 157:116808. [PMID: 36751553 PMCID: PMC7614147 DOI: 10.1016/j.trac.2022.116808] [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] [Indexed: 11/06/2022]
Abstract
Cardiolipin (CL) is a mitochondria-exclusive phospholipid, primarily localised within the inner mitochondrial membrane, that plays an essential role in mitochondrial architecture and function. Aberrant CL content, structure, and localisation have all been linked to impaired mitochondrial activity and are observed in the pathophysiology of cancer and neurological, cardiovascular, and metabolic disorders. The detection, quantification, and localisation of CL species is a valuable tool to investigate mitochondrial dysfunction and the pathophysiological mechanisms underpinning several human disorders. CL is measured using liquid chromatography, usually combined with mass spectrometry, mass spectrometry imaging, shotgun lipidomics, ion mobility spectrometry, fluorometry, and radiolabelling. This review summarises available methods to analyse CL, with a particular focus on modern mass spectrometry, and evaluates their advantages and limitations. We provide guidance aimed at selecting the most appropriate technique, or combination of techniques, when analysing CL in different model systems, and highlight the clinical contexts in which measuring CL is relevant.
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Affiliation(s)
- Javier S. Bautista
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Padraig J. Flannery
- Neurometabolic Unit, The National Hospital for Neurology and Neurosurgery, London, UK,Neurogenetics Unit, Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, London, UK
| | - Michael G. Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Simon J.R. Heales
- Neurometabolic Unit, The National Hospital for Neurology and Neurosurgery, London, UK,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon A.S. Pope
- Neurometabolic Unit, The National Hospital for Neurology and Neurosurgery, London, UK,Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Robert D.S. Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK, Corresponding author. Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK. (R.D.S. Pitceathly)
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7
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Criscuolo A, Nepachalovich P, Garcia-del Rio DF, Lange M, Ni Z, Baroni M, Cruciani G, Goracci L, Blüher M, Fedorova M. Analytical and computational workflow for in-depth analysis of oxidized complex lipids in blood plasma. Nat Commun 2022; 13:6547. [PMID: 36319635 PMCID: PMC9626469 DOI: 10.1038/s41467-022-33225-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 09/05/2022] [Indexed: 11/06/2022] Open
Abstract
Lipids are a structurally diverse class of biomolecules which can undergo a variety of chemical modifications. Among them, lipid (per)oxidation attracts most of the attention due to its significance in the regulation of inflammation, cell proliferation and death programs. Despite their apparent regulatory significance, the molecular repertoire of oxidized lipids remains largely elusive as accurate annotation of lipid modifications is complicated by their low abundance and often unknown, biological context-dependent structural diversity. Here, we provide a workflow based on the combination of bioinformatics and LC-MS/MS technologies to support identification and relative quantification of oxidized complex lipids in a modification type- and position-specific manner. The developed methodology is used to identify epilipidomics signatures of lean and obese individuals with and without type 2 diabetes. The characteristic signature of lipid modifications in lean individuals, dominated by the presence of modified octadecanoid acyl chains in phospho- and neutral lipids, is drastically shifted towards lipid peroxidation-driven accumulation of oxidized eicosanoids, suggesting significant alteration of endocrine signalling by oxidized lipids in metabolic disorders.
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Affiliation(s)
- Angela Criscuolo
- grid.9647.c0000 0004 7669 9786Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany ,grid.424957.90000 0004 0624 9165Thermo Fisher Scientific, 63303 Dreieich, Germany
| | - Palina Nepachalovich
- grid.4488.00000 0001 2111 7257Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany ,grid.9647.c0000 0004 7669 9786Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany
| | - Diego Fernando Garcia-del Rio
- grid.9647.c0000 0004 7669 9786Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany
| | - Mike Lange
- grid.9647.c0000 0004 7669 9786Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany
| | - Zhixu Ni
- grid.4488.00000 0001 2111 7257Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany ,grid.9647.c0000 0004 7669 9786Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany
| | - Massimo Baroni
- grid.452579.8Molecular Discovery, Kinetic Business Centre, Borehamwood, WD6 4PJ Hertfordshire UK
| | - Gabriele Cruciani
- grid.9027.c0000 0004 1757 3630Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Laura Goracci
- grid.9027.c0000 0004 1757 3630Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Matthias Blüher
- grid.9647.c0000 0004 7669 9786Medical Department III (Endocrinology, Nephrology and Rheumatology), University of Leipzig, 04103 Leipzig, Germany ,grid.411339.d0000 0000 8517 9062Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, 04103 Leipzig, Germany
| | - Maria Fedorova
- grid.4488.00000 0001 2111 7257Center of Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany ,grid.9647.c0000 0004 7669 9786Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, 04013 Leipzig, Germany ,grid.9647.c0000 0004 7669 9786Center for Biotechnology and Biomedicine, University of Leipzig, 04013 Leipzig, Germany
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8
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He Y, Yuan B, Lu Y, Zhao X, Shen C, Ji J, Lin L, Xu J, Xie T, Shan J. In-silico-library-based method enables rapid and comprehensive annotation of cardiolipins and cardiolipin oxidation products using high resolution tandem mass spectrometer. Anal Chim Acta 2021; 1180:338879. [PMID: 34538317 DOI: 10.1016/j.aca.2021.338879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 01/18/2023]
Abstract
Accumulated evidences suggest that cardiolipins (CLs) and cardiolipin oxidation products (oxCLs) are a class of essential molecules that play critical roles in many physiological functions. Diversity of four acyl chains leads to high structure complexity for cardiolipin species including CLs, monolysocardiolipins (MLCLs) and their oxCLs. The ability to rapidly identify CL species can be implemented by the match of mass spectrometry (MS)-based in-silico spectral database. In this study, after optimizing the chromatography conditions and MS detection, an in-silico library containing 377,754 simulated tandem mass spectra deducing from 31,578 CLs to 52,160 of MLCLs was successfully augmented based on LipidBlast templates. For the construction of the oxCLs' library, twenty-five fatty acyls oxidation products relating to nine oxidation types were permuted and combined. A total of 42,180 oxCL spectra were predicted based on the experimental measurements of oxCLs forming by artificially oxidation. Applying the in-silico database to murine mitochondria and cell samples enabled the sensitive and comprehensive annotation of 86 MLCLs, 307 CLs and 112 oxCLs with high annotation confidence. Compared to the conventional method, our proposed in-silico database provides a more comprehensive interpretation for CL species' characterization with high throughput and sensitivity in nontarget lipidomic study.
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Affiliation(s)
- Yu He
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Binghuan Yuan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yao Lu
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xia Zhao
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Cunsi Shen
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jianjian Ji
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Lili Lin
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jianya Xu
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Tong Xie
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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9
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Barker-Tejeda TC, Villaseñor A, Gonzalez-Riano C, López-López Á, Gradillas A, Barbas C. In vitro generation of oxidized standards for lipidomics. Application to major membrane lipid components. J Chromatogr A 2021; 1651:462254. [PMID: 34118530 DOI: 10.1016/j.chroma.2021.462254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/09/2021] [Accepted: 05/11/2021] [Indexed: 12/22/2022]
Abstract
Membrane lipids (sphingolipids, glycerophospholipids, cardiolipins, and cholesteryl esters) are critical in cellular functions. Alterations in the levels of oxidized counterparts of some of these lipids have been linked to the onset and development of many pathologies. Unfortunately, the scarce commercial availability of chemically defined oxidized lipids is a limitation for accurate quantitative analysis, characterization of oxidized composition, or testing their biological effects in lipidomic studies. To address this dearth of standards, several approaches rely on in-house prepared mixtures of oxidized species generated under in vitro conditions from different sources - non-oxidized commercial standards, liposomes, micelles, cells, yeasts, and human preparations - and using different oxidant systems - UVA radiation, air exposure, enzymatic or chemical oxidant systems, among others. Moreover, high-throughput analytical techniques such as liquid chromatography coupled to mass spectrometry (LC-MS) have provided evidence of their capabilities to study oxidized lipids both in in vitro models and complex biological samples. In this review, we describe the commercial resources currently available, the in vitro strategies carried out for obtaining oxidized lipids as standards for LC-MS analysis, and their applications in lipidomics studies, specifically for lipids found in cell and mitochondria membranes.
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Affiliation(s)
- Tomás Clive Barker-Tejeda
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain; Institute of Applied Molecular Medicine (IMMA), Department of Basic Medical Science, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain.
| | - Alma Villaseñor
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain; Institute of Applied Molecular Medicine (IMMA), Department of Basic Medical Science, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain.
| | - Carolina Gonzalez-Riano
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain.
| | - Ángeles López-López
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain.
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain.
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid. Spain.
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10
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Vítová M, Stránská M, Palyzová A, Řezanka T. Detailed structural characterization of cardiolipins from various biological sources using a complex analytical strategy comprising fractionation, hydrolysis and chiral chromatography. J Chromatogr A 2021; 1648:462185. [PMID: 33984647 DOI: 10.1016/j.chroma.2021.462185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 12/14/2022]
Abstract
Cardiolipins (1,3-bis(sn-3'-phosphatidyl)-sn-glycerol) (CLs) are widespread in many organisms, from bacteria to higher green plants and mammals. CLs were observed in Gram-positive bacterium of the genus Kocuria, brewer's yeast Saccharomyces, the green alga Chlamydomonas, spinach and beef heart. A mixture of molecular species of CLs was obtained from total lipids by hydrophilic interaction liquid chromatography (HILIC), and these were further separated and identified by reversed phase LC/MS with negative tandem electrospray ionization. The majority of CLs molecular species from each organism were cleaved using phospholipase C from Bacillus cereus. This phospholipase cleaves CLs into 1,2-diglycerols and phosphatidylglycerol 3-phosphates, which were then separated. After CLs cleavage, diacylglycerols such as sn-1,2-diacyl-3-acetyl-glycerols (i.e., triacylglycerols) were separated and identified by chiral chromatography/MS-positive tandem ESI. Significant differences in the composition of the molecular species between the 3-(3-sn-phosphatidyl) and 1-(3-sn-phosphatidyl) moieties of CLs were found in all organisms tested. Molecular species of CLs that contained four different fatty acids were identified in all five samples, and CLs containing very long chain fatty acids were identified in yeast. In addition, CLs containing both enantiomers (at the sn-2 carbon) were present in the bacterium tested. These findings were further supported by data already published in GenBank where, in the same family - Micrococcaceae - both enzymes responsible for chirality in the sn-2 position, glycerol-3-phosphate and glycerol-1-phosphate dehydrogenases, were present.
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Affiliation(s)
- Milada Vítová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, Novohradská 237, 379 81 Třeboň, Czech Republic
| | - Milena Stránská
- University of Chemistry and Technology Prague, Faculty of Food and Biochemical Technology, Department of Food Analysis and Nutrition, Technická 3, 166 28 Prague, Czech Republic
| | - Andrea Palyzová
- University of Chemistry and Technology Prague, Faculty of Food and Biochemical Technology, Department of Food Analysis and Nutrition, Technická 3, 166 28 Prague, Czech Republic
| | - Tomáš Řezanka
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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11
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Strife RJ, Campbell S, Price JM, Motlagh S. Normalized Mass Maps in Three-Dimensional Space Combining Kendrick-like Values with Chromatographic Separation for Enhanced Data Deconvolution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:989-995. [PMID: 33733763 DOI: 10.1021/jasms.0c00481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The incorporation of retention-time information into a fully rotatable and interactive three-dimensional (3D), "Kendrick-like" normalized mass map (NMM) using a single software platform is reported. Surprising discoveries were made about the elution pattern of block ethoxylate-propoxylate oligomers (ca. 2800 Da) in the supercritical fluid after combined SFC-Orbitrap FTMS analysis. The 3D NMM also facilitated identification of impurities using interactive graphics tools within the map. By selecting map glyphs, associated reconstructed ion chromatograms were automatically generated. Last, since Kendrick and Kendrick-like mapping (NMM) are chemical-formula-based, incorporating retention time in 3D space allows the possibility of resolving isomers in the map.
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Affiliation(s)
- Robert J Strife
- Sierra Analytics, 5815 Stoddard Road, Suite 601, Modesto, California 95356, United States
| | - Scott Campbell
- Sierra Analytics, 5815 Stoddard Road, Suite 601, Modesto, California 95356, United States
| | - Jason M Price
- Mass Spectrometry Laboratory, Corporate Functions-Analytical, The Procter & Gamble Co., 8700 Mason-Montgomery Road, Mason, Ohio 45040, United States
| | - Safa Motlagh
- Mass Spectrometry Laboratory, Corporate Functions-Analytical, The Procter & Gamble Co., 8700 Mason-Montgomery Road, Mason, Ohio 45040, United States
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12
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Helmer PO, Nordhorn ID, Korf A, Behrens A, Buchholz R, Zubeil F, Karst U, Hayen H. Complementing Matrix-Assisted Laser Desorption Ionization-Mass Spectrometry Imaging with Chromatography Data for Improved Assignment of Isobaric and Isomeric Phospholipids Utilizing Trapped Ion Mobility-Mass Spectrometry. Anal Chem 2021; 93:2135-2143. [PMID: 33416303 DOI: 10.1021/acs.analchem.0c03942] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Lipids, such for example the multifaceted category of glycerophospholipids (GP), play a major role in many biological processes. High-resolution mass spectrometry is able to identify these highly diverse lipid species in combination with fragmentation experiments (MS/MS) on the basis of the accurate m/z and fragmentation pattern. However, for the differentiation of isomeric lipids or isobaric interferences, more elaborate separation methods are required. Especially for imaging techniques, such as matrix-assisted laser desorption/ionization (MALDI)-MS imaging, the identification is often exclusively based on the accurate m/z. Fragmentation via MS/MS increases the confidence in lipid annotation in imaging approaches. However, this is sometimes not feasible due to insufficient sensitivity and significantly prolonged analysis time. The use of a separation dimension such as trapped ion mobility spectrometry (TIMS) after ionization strengthens the confidence of the identification based on the collision cross section (CCS). Since CCS libraries are limited, a tissue-specific database was initially generated using hydrophilic interaction liquid chromatography-TIMS-MS. Using this database, the identification of isomeric lipid classes as well as isobaric interferences in a lipid class was performed using a mouse spleen sample in a workflow described in this study. Besides a CCS-based identification as an additional identification criterion for GP in general, the focus was on the distinction of the isomeric GP classes phosphatidylglycerol and bis(monoacylglycero)phosphate, as well as the differentiation of possible isobaric interferences based on the formation of adducts by MALDI-TIMS-MS imaging on a molecular level.
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Affiliation(s)
- Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Ilona D Nordhorn
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Ansgar Korf
- Bruker Daltonik GmbH, Fahrenheitstraße 4, Bremen 28359, Germany
| | - Arne Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Rebecca Buchholz
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Florian Zubeil
- Bruker Daltonik GmbH, Fahrenheitstraße 4, Bremen 28359, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstraße 30, Münster 48149, Germany
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13
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Helmer PO, Nicolai MM, Schwantes V, Bornhorst J, Hayen H. Investigation of cardiolipin oxidation products as a new endpoint for oxidative stress in C. elegans by means of online two-dimensional liquid chromatography and high-resolution mass spectrometry. Free Radic Biol Med 2021; 162:216-224. [PMID: 33127566 DOI: 10.1016/j.freeradbiomed.2020.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/29/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022]
Abstract
The investigation of neurodegenerative and age-related diseases is a highly relevant topic in current research. Especially oxidative stress is thought to be the common underlying mechanism in diseases such as Parkinson's or Alzheimer's disease. The nematode Caenorhabditis elegans (C. elegans) is a prominent model organism, which is often used for such investigations and has gained extensive recognition in research regarding the linkage of reactive oxygen species (ROS) and neurodegeneration. Not only studies regarding genomics and proteomics have been increasingly conducted, also the number of studies based on the lipidome is rising. The phospholipid class of cardiolipin (CL) is a unique lipid class, which is exclusively located in mitochondria and is therefore of great relevance regarding oxidative stress and associated diseases. CL oxidation products have become a prominent marker for oxidative stress in various organisms. However, the CL distribution in the nematode C. elegans is still scarcely known on the molecular level and oxidation products have not yet been identified. In this work, we demonstrate the importance of CL distribution and the applicability of CL oxidation products as a sensitive marker for oxidative stress in C. elegans. For this reason, the CL distribution was determined by means of online two-dimensional liquid chromatography hyphenated with high-resolution mass spectrometry (2D-LC/HRMS). Subsequently, worms were treated with tert-butyl hydroperoxide (tBOOH) in order to provoke oxidative stress and induce the artificial formation of oxidized CL. We were able to detect increasing amounts of CL oxidation products of highly unsaturated CL species in a concentration-dependent manner. This finding emphasizes the great potential of CL oxidation products as a sensitive marker substance of oxidative stress in C. elegans, which is not only directly linked to mitochondria function but also favourable to other oxidative stress markers in terms of the needed sample material, relative substance stability and specificity of the oxidation site.
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Affiliation(s)
- Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Merle M Nicolai
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany; TraceAge - DFG Research Unit FOR, 2558, Berlin-Potsdam-Jena, Germany
| | - Vera Schwantes
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149, Münster, Germany
| | - Julia Bornhorst
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany; TraceAge - DFG Research Unit FOR, 2558, Berlin-Potsdam-Jena, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149, Münster, Germany.
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14
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Helmer PO, Behrens A, Rudt E, Karst U, Hayen H. Hydroperoxylated vs Dihydroxylated Lipids: Differentiation of Isomeric Cardiolipin Oxidation Products by Multidimensional Separation Techniques. Anal Chem 2020; 92:12010-12016. [PMID: 32867498 DOI: 10.1021/acs.analchem.0c02605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, cardiolipin (CL) oxidation products were recognized as potential markers for mitochondrial dysfunction in conjunction with age related diseases. The analysis of oxidized CL requires powerful analysis techniques due to high structural diversity. In addition, low concentrations of partly labile compounds pose a special challenge, supplemented by the occurrence of isomeric compounds, e.g., hydroperoxylated vs dihydroxylated products. Therefore, we present a hyphenated method based on liquid chromatography coupled to trapped ion mobility spectrometry (TIMS) for separation and tandem mass spectrometry (MS/MS) for structural characterization. This enables comprehensive analysis of an artificially oxidized CL extract of bovine heart. Isomeric oxidation products could be differentiated by mobility-resolved MS/MS fragmentation experiments. Our developed method could help to better understand the physiological role of oxidized CL.
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Affiliation(s)
- Patrick O Helmer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Arne Behrens
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Edward Rudt
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Uwe Karst
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Corrensstr. 30, 48149 Münster, Germany
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15
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Aldana J, Romero-Otero A, Cala MP. Exploring the Lipidome: Current Lipid Extraction Techniques for Mass Spectrometry Analysis. Metabolites 2020; 10:metabo10060231. [PMID: 32503331 PMCID: PMC7345237 DOI: 10.3390/metabo10060231] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/05/2020] [Accepted: 05/13/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, high-throughput lipid profiling has contributed to understand the biological, physiological and pathological roles of lipids in living organisms. Across all kingdoms of life, important cell and systemic processes are mediated by lipids including compartmentalization, signaling and energy homeostasis. Despite important advances in liquid chromatography and mass spectrometry, sample extraction procedures remain a bottleneck in lipidomic studies, since the wide structural diversity of lipids imposes a constrain in the type and amount of lipids extracted. Differences in extraction yield across lipid classes can induce a bias on down-stream analysis and outcomes. This review aims to summarize current lipid extraction techniques used for untargeted and targeted studies based on mass spectrometry. Considerations, applications, and limitations of these techniques are discussed when used to extract lipids in complex biological matrices, such as tissues, biofluids, foods, and microorganisms.
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