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The field of lipidomics has undergone an enormous growth in recent years, which can be illustrated by the number of published articles and other bibliometric parameters. This highlights the renewed interest in lipids, now driven by the enthusiasm to explore the world of lipidomes and how these, among others, impact health and disease. The excitement is enormous, prompting many newcomers to enter the field. However, training and education in lipidomics are still scarce or even lacking. A successful lipidomics study requires appropriate expertise in all aspects of the lipidomic workflow, covering experimental design, sample preparation, analytical measurement using mass spectrometry techniques, data processing, and finally correct reporting of lipidomic results. The large discrepancy in know‐how and lipidomics assessments causes confusion in the field that is also mirrored in the literature. Recently, the International Lipidomics Society was established to fill this gap and to unite researchers around the world interested in all aspects of lipidomics research and collectively start creating urgently needed textbook chapters in lipidomics. This situation prompted us to start working on this book project, where we have assembled the content covering three sections: analytical methodologies in lipidomics, lipidomic analysis according to lipid categories and classes, and finally lipidomic applications. We invited leading experts for particular topics, and, after more than a year of tedious work, we are proud to present the resul
Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Mass Spectrometry for Lipidomics Methods and Applications Edited by Michal Holčapek and Kim Ekroos Volume Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Mass Spectrometry for Lipidomics Methods and Applications Edited by Michal Holčapek and Kim Ekroos Volume Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Mass Spectrometry for Lipidomics Dr Kim Ekroos Library of Congress Card No.: applied for Dr Michal Holčapek Lipidomics Consulting Ltd Irisviksvägen 31D 02230 Espoo Finland Cover Design: Wiley Cover Images: © Kateryna Kon/Shutterstock; Courtesy of Michaela Chocholoušková British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library Bibliographic information published by the Deutsche Nationalbibliothek The Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at â 2023WileyVCH GmbH, Boschstraòe 12, 69469 Weinheim, Germany All rights reserved (including those of translation into other languages) No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers Registered names, trademarks, etc used in this book, even when not specifically marked as such, are not to be considered unprotected by law Print ISBN: 978-3-527-35222-7 ePDF ISBN: 978‐3‐527‐83649‐9 ePub ISBN: 978‐3‐527‐83650‐5 oBook ISBN: 978‐3‐527‐83651‐2 Typesetting Straive, Chennai, India Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License University of Pardubice Faculty of Chemical Technology Studentská 573 53210 Pardubice Czech Republic All books published by WILEY-VCH are carefully produced Nevertheless, authors, editors, and publisher not warrant the information contained in these books, including this book, to be free of errors Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate Editors Contents Preface xiii 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Introduction to Lipidomics Harald C Köfeler, Kim Ekroos, and Michal Holčapek Preface Historical Perspective Sampling and Preanalytics Reference Materials and Biological Reference Ranges Clinical Lipidomics Identification and Annotation Quantitation Lipid Ontology 10 References 11 Part I Analytical Methodologies in Lipidomics 13 2.1 2.2 2.3 2.4 2.5 2.5.1 2.5.2 2.5.3 2.5.4 2.5.5 2.6 2.6.1 2.6.2 2.6.3 Preanalytics forLipidomics Analysis 15 Gonỗalo Vale and Jeffrey G McDonald Safety 15 Introduction 15 Sample Origin 16 Sample Collection 17 Tissue Homogenization 19 Mortar and Pestle 20 Rotor–Stator 21 Blender 21 Potter-Elvehjem 22 Bead Mill 22 Liquid–Liquid Extraction (LLE) 22 Folch Method 24 Bligh and Dyer (BD) Method 27 Modified Folch and Bligh/Dyer (BD) Methods 27 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License v Contents 2.6.4 2.6.5 2.6.6 2.6.7 2.6.8 2.7 2.8 2.9 Rose and Oaklander (RO) Method 28 Matyash or Methyl-tert-Butyl Ether (mTBE) Method 28 BUME Method 28 Alshehry Method 29 Three-Phase Lipid Extraction (3PLE) 29 Resuspension and Solubilization 30 Automation 31 Tips and Tricks 34 References 38 Direct Infusion (Shotgun) Electrospray Mass Spectrometry 41 Marcus Höring and Gerhard Liebisch Introduction 41 Complexity of Crude Lipid Extracts 42 Main Lipid Classes in Mammalian Samples 42 Bond Types as Structural Features 43 Fatty Acids as the Major Building Blocks 44 Lipid Species and Double-Bond Series 45 Introduction to Mass Spectrometry of Lipids 46 Annotation of Lipid Structures Analyzed by MS 46 Isomers 48 Isobars and the Type-II Isotopic Overlap 49 Overview of Direct Infusion MS Workflows 50 Sample Preparation 50 Preanalytics – Sample Stability 50 Lipid Extraction 54 Solvents, Additives, and Lipid Concentration 54 Sample Derivatization 55 Direct Infusion 55 Mass Spectrometry Analysis 56 Electrospray Ionization of Lipids 56 Tandem Mass Spectrometry 57 Multidimensional MS Shotgun Lipidomics 61 High-Resolution Mass Spectrometry 61 Lipid Identification 65 Identification by MS/MS 65 Identification by HRMS 65 Consideration of Type-II Overlap 67 Identification Hierarchy 67 Caveats/Pitfalls 69 Lipid Quantification 70 Internal Standards 70 Type-I Isotopic Effect 71 Evaluation and Correction of Isotopic Overlap 71 Species Response 73 3.1 3.2 3.2.1 3.2.2 3.2.3 3.2.4 3.3 3.3.1 3.3.2 3.3.3 3.4 3.5 3.5.1 3.5.2 3.5.3 3.5.4 3.6 3.7 3.7.1 3.7.2 3.7.3 3.7.4 3.8 3.8.1 3.8.2 3.8.3 3.8.4 3.8.5 3.9 3.9.1 3.9.2 3.9.3 3.9.4 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License vi 3.9.5 3.10 3.11 3.12 3.12.1 3.12.2 3.12.3 3.13 Calculation of Concentration 76 Data Analysis/Software 78 Limitations 79 Selected Applications 79 Analysis of Plasma 79 Analysis of Tissues and Cells 80 Analysis of Lipid Metabolism 80 Outlook 81 References 82 Liquid Chromatography – and Supercritical Fluid Chromatography – Mass Spectrometry 91 Michal Holčapek, Ondřej Peterka, Michaela Chocholoušková, and Denise Wolrab Introduction 91 Lipid Class Separation 93 Normal-Phase Liquid Chromatography 94 Hydrophilic Interaction Liquid Chromatography 95 Supercritical Fluid Chromatography 97 Lipid Species Separation 99 Reversed-Phase Liquid Chromatography 99 Nonaqueous Reversed-Phase Liquid Chromatography 102 Other Separation Approaches 103 Silver Ion Chromatography 103 Chiral Chromatography 105 Multidimensional Approaches 106 References 108 4.1 4.2 4.2.1 4.2.2 4.2.3 4.3 4.3.1 4.3.2 4.4 4.4.1 4.4.2 4.4.3 Mass Spectrometry Imaging of Lipids 117 Shane R Ellis and Jens Soltwisch 5.1 Introduction 117 5.2 Sample Preparation for Mass Spectrometry Imaging of Lipids 118 5.2.1 Tissue Samples 118 5.2.2 Sectioning and Mounting 119 5.2.3 Cell Culture 119 5.2.4 Pre-processing 119 5.2.5 Handling and Storage 120 5.2.6 Formalin-Fixed Paraffin-Embedded Tissue 120 5.3 Desorption/Ionization Techniques used for MSI of Lipids 120 5.3.1 Matrix-Assisted Laser Desorption/Ionization (MALDI) 120 5.3.2 Secondary Ion Mass Spectrometry SIMS 124 5.3.3 MSI Methods Using Electrospray Ionization 125 5.3.3.1 Desorption Electrospray Ionization 125 5.3.3.2 Laser Ablation Electrospray Ionization and IR-Matrix-Assisted Laser Desorption-Electrospray Ionization 127 vii Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Contents Contents 5.3.3.3 5.4 5.5 5.6 5.7 5.7.1 5.7.2 5.7.3 5.7.4 5.7.5 5.8 Nanospray Desorption Electrospray Ionization 128 Combining Ion Mobility of Lipids with MSI 128 On Tissue Chemical Derivatization for MSI 129 Quantification in MSI 130 Lipid Identification for MSI 132 Types of Ions Generated by MSI 132 In-source Fragmentation Considerations 133 MSI Lipid Identification Using Accurate Mass 133 Deploying MS/MS for Lipid Identification in MSI 135 Isomer-Resolved MSI 135 Conclusions 137 References 137 Ion Mobility Spectrometry 151 Kaylie I Kirkwood, Melanie T Odenkirk, and Erin S Baker Ion Mobility Spectrometry 151 Introduction 151 Ion Mobility Spectrometry Techniques and Platforms 154 Drift Tube Ion Mobility Spectrometry (DTIMS) 154 Traveling-Wave Ion Mobility Spectrometry (TWIMS) 156 Trapped Ion Mobility Spectrometry (TIMS) 157 Field Asymmetric Ion Mobility Spectrometry (FAIMS) 158 Ion Mobility Resolving Power (Rp) Advancements 159 Cyclic IMS (cIM) 159 Standard Lossless Ion Manipulation (SLIM) 160 Tandem IMS 161 IMS Data Deconvolution Software Strategies 161 Drift Gas Dopants and Modifiers 163 Benefits of IMS for Lipidomics 164 Chemical Space Separation with IMS 165 Lipid Identification and Characterization with CCS 166 CCS for Lipid Structural Analysis 168 Lipidomic Applications with IMS 168 IMS in Imaging and Shotgun Lipidomics 168 IMS-MS/MS and Novel Speciation Approaches 169 Conclusions and Outlook of IMS for Lipidomics 172 References 173 6.1 6.1.1 6.1.2 6.1.2.1 6.1.2.2 6.1.2.3 6.1.2.4 6.1.3 6.1.3.1 6.1.3.2 6.1.3.3 6.1.3.4 6.1.3.5 6.1.4 6.1.4.1 6.1.4.2 6.1.4.3 6.1.5 6.1.5.1 6.1.5.2 6.1.6 Structural Characterization of Lipids Using Advanced Mass Spectrometry Approaches 183 Josef Cvačka, Vladimír Vrkoslav, and Štěpán Strnad 183 7.1 Introduction 183 7.2 Structure and Position of Aliphatic Chains in Lipids 185 7.2.1 Double and Triple Bonds 185 7.2.1.1 Charge-Switch Derivatization of Fatty Acids 186 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License viii 7.2.1.2 7.2.1.3 7.2.1.4 7.2.1.5 7.2.1.6 7.2.1.7 7.2.2 7.2.3 7.2.4 7.3 Ozone-Induced Dissociation 187 Paternò–Büchi Reaction 192 Epoxidation of Double Bonds 194 Acetonitrile-Related Adducts in APCI 195 Photodissociation of Unsaturated Lipids 199 Electron-Induced Dissociation of Unsaturated Lipids 202 Methyl Branching of Aliphatic Chains 204 Oxygen-Containing Functional Groups and Carbocyclic Structures 205 Stereospecific Position of Acyl Chain on Glycerol 207 Conclusions and Outlook 210 References 211 Lipidomic Identification 227 Harald Köfeler Overview 227 Chromatography 228 Mass Spectrometry 230 Exact Mass 230 Fragment Spectra 232 General Considerations 232 Fatty Acids 233 Oxylipins 233 Phospholipids 234 Sphingolipids 237 Glycerolipids 242 Sterols 242 Deep Structure Determination 242 Ion Mobility Spectrometry 243 Identification Workflows 244 References 249 8.1 8.2 8.3 8.3.1 8.3.2 8.3.2.1 8.3.2.2 8.3.2.3 8.3.2.4 8.3.2.5 8.3.2.6 8.3.2.7 8.3.3 8.4 8.5 9.1 9.2 9.3 9.4 9.4.1 9.4.2 9.5 9.5.1 9.5.2 9.6 9.7 Lipidomics Quantitation 255 Michaela Chocholoušková, Denise Wolrab, Ondřej Peterka, Robert Jirásko, and Michal Holčapek Introduction to Lipidomics Quantitation 255 Principle of Quantitation 256 Internal Standards 257 Isotopic Correction 261 Isotopic Correction Type I 261 Isotopic Correction Type II 262 Common Approaches for Lipidomics Quantitation 263 Shotgun MS 263 Chromatography – MS 264 Validation 265 Quality Control (QC) 268 References 268 ix Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Contents 75 Danne-Rasche, N., Rubenzucker, S., and Ahrends, R (2020) Uncovering the complexity of the yeast lipidome by means of nLC/NSI-MS/MS Anal Chim Acta 1140: 199–209 76 Zhang, W., Zhang, D., Chen, Q et al (2019) Online photochemical derivatization enables comprehensive mass spectrometric analysis of unsaturated phospholipid isomers Nat Commun 10 (1): 1–9 77 Kuo, T.-H., Chung, H.-H., Chang, H.-Y et al (2019) Deep lipidomics and molecular imaging of unsaturated lipid isomers: a universal strategy initiated by mCPBA epoxidation Anal Chem 91 (18): 11905–11915 78 Thomas, M.C., Mitchell, T.W., Harman, D.G et al (2008) Ozone-induced dissociation: elucidation of double bond position within mass-selected lipid ions Anal Chem 80 (1): 303–311 79 Takahashi, H., Shimabukuro, Y., Asakawa, D et al (2018) Structural analysis of phospholipid using hydrogen abstraction dissociation and oxygen attachment dissociation in tandem mass spectrometry Anal Chem 90 (12): 7230–7238 80 Uchino, H., Tsugawa, H., Takahashi, H., and Arita, M (2021) Computational Mass Spectrometry Accelerates C=C Position-Resolved Untargeted Lipidomics Using Oxygen Attachment Dissociation Research Square https://doi.org/10.21203/ rs.3.rs-727852/v1 81 Baba, T., Campbell, J.L., Le Blanc, J.C.Y., and Baker, P.R.S (2017) Distinguishing cis and trans isomers in intact complex lipids using electron impact excitation of ions from organics mass spectrometry Anal Chem 89 (14): 7307–7315 82 Williams, P.E., Klein, D.R., Greer, S.M., and Brodbelt, J.S (2017) Pinpointing double bond and sn-positions in glycerophospholipids via hybrid 193 nm ultraviolet photodissociation (UVPD) mass spectrometry J Am Chem Soc 139 (44): 15681–15690 83 Klein, D.R., Blevins, M.S., Macias, L.A et al (2020) Localization of double bonds in bacterial glycerophospholipids using 193 nm ultraviolet photodissociation in the negative mode Anal Chem 92 (8): 5986–5993 84 Blevins, M.S., James, V.K., Herrera, C.M et al (2020) Unsaturation elements and other modifications of phospholipids in bacteria: new insight from ultraviolet photodissociation mass spectrometry Anal Chem 92 (13): 9146–9155 85 Brodbelt, J.S., Morrison, L.J., and Santos, I (2020) Ultraviolet photodissociation mass spectrometry for analysis of biological molecules Chem Rev 120 (7): 3328–3380 86 Watrous, J., Roach, P., Alexandrov, T et al (2012) Mass spectral molecular networking of living microbial colonies Proc Natl Acad Sci U.S.A 109 (26): E1743–E1752 87 Fox Ramos, A.E., Evanno, L., Poupon, E et al (2019) Natural products targeting strategies involving molecular networking: different manners, one goal Nat Prod Rep 36 (7): 960–980 88 Quinn, R.A., Melnik, A.V., Vrbanac, A et al (2020) Global chemical effects of the microbiome include new bile-acid conjugations Nature 579 (7797): 123–129 703 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Reference 27 Microbial Lipidomics 89 Cajka, T and Fiehn, O (2016) Toward merging untargeted and targeted methods in mass spectrometry-based metabolomics and lipidomics Anal Chem 88 (1): 524–545 90 Sarafian, M.H., Gaudin, M., Lewis, M.R et al (2014) Objective set of criteria for optimization of sample preparation procedures for ultra-high throughput untargeted blood plasma lipid profiling by ultra performance liquid chromatography-mass spectrometry Anal Chem 86 (12): 5766–5774 91 Wong, M.W.K., Braidy, N., Pickford, R et al (2019) Comparison of single phase and biphasic extraction protocols for lipidomic studies using human plasma Front Neurol 10: 879 92 Lipidomics Standards Initiative Consortium (2019) Lipidomics needs more standardization Nat Metab (8): 745–747 93 O’Donnell, V.B., Ekroos, K., Liebisch, G., and Wakelam, M (2020) Lipidomics: current state of the art in a fast moving field Wiley Interdiscip Rev Syst Biol Med 12 (1): e1466 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 704 Index a acetonitrile 29, 94, 95, 99, 101, 102, 106, 185, 195, 196, 296, 329, 490, 493, 497, 500, 535, 591 acyl alpha‐hydroxy fatty acid (AAHFA) 697 acyl phosphatidylglycerol 416–417 adipocytes 42, 46, 641 advanced mass spectrometry 183–211 aging/ageing process 657–658 Alzheimer’s disease 660–661 chronological and metabolic 662–663 development and application of 663–664 plasma lipidome 659 using lipidomics 658–659 Alshehry method 29 Alzheimer’s disease 660–661 vs lipids 661–662 anionic lysoglycerophospholipids 416 anticoagulants 18, 322, 562 antioxidants 18, 321, 548, 562, 571, 591 apolipoprotein E gene (APOE) 661 Arabidopsis thaliana 601, 608, 610 argentation chromatography 103 arylsulfatase A (ARSA) 427, 455 assay design and raw data analysis with LipidCreator and Skyline 276–278 with LipidXplorer 279–280 atmospheric pressure ionization (API) techniques 186, 354, 356, 362, 364 atmospheric pressure photoionization (APPI) 102 b bead mill 22 benzophenone 137, 193, 194 bile acids (BAs) 509, 693–694 amphiphilic nature 510 analytical methods 512–517 applications 516 disadvantage 516 GC‐MS 517–518 human hepatocytes 509 LC‐MS early technologies and ESI‐ Quadrupole MS 518–519 HR‐MS 519 SFC 519–520 microbiome research 512 synthesis 511 bis(monoacylglycero)phosphate (BMP) 55, 395, 413–414 blender homogenizer 21 Bligh and Dyer (BD) method 23, 27–28 branched‐chain fatty acids (BCFA) 204, 296, 305, 307 butanol–methanol (BUME) method 24, 28–29 butylhydroxytoluene (BHT) 18 Mass Spectrometry for Lipidomics: Methods and Applications, First Edition Edited by Michal Holčapek and Kim Ekroos © 2023 WILEY-VCH GmbH Published 2023 by WILEY-VCH GmbH Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 705 Index c cancer biomarkers 546 cancer lipidomics in biological samples 546–547 data processing 551–552 and data reporting 551–552 method requirements 549–550 preanalytical considerations 547–548 in research 552–554 sample preparation 549 statistical analysis 551–552 validation and quality control 550–551 carboxymethylcellulose (CMC) 118 cardiolipin (CL) 56, 134, 169, 170, 395, 415–416, 676, 691 cells analysis 80 ceramides with long and very long acyl chains 435–440 1‐phosphates 443–444 skin omega‐hydroxy 440–441 ceramide synthases 427, 429, 436, 440, 457, 461, 672, 674 charge‐inversion approach 137 charge transfer dissociation (CTD) 204 chemical ionization 185, 305, 444, 516, 517, 647 chiral chromatography 9, 105–106, 227, 329–331, 353, 364, 369 cholesterol esters 94, 229, 500, 501, 510 cholesterol precursors 485 cholesteryl ester (CEs) 23, 42, 77, 256, 535, 536, 540, 628, 650 choline glycerophospholipid alkaline adducts 401–402 protonated species 400–401 choline lysoglycerophospholipids (lysoPC) 403–405 chromatographic separation 48, 50, 67, 71, 107, 227–230, 232, 242, 263, 274, 318, 325, 490, 519, 591, 694 chromatography coupling 256 chromatography MS 264–265 chromatography technology 696 chronological age 659, 662–663 CID spectrum 234 circular economy model 593, 595 citrate 18, 120, 646 clinical diagnostics 557 congenital adrenal hyperplasia (CAH) 569–570 Fabry disease 567 F2‐Isoprostanes 571 Gaucher disease 568 intrahepatic cholestasis of pregnancy (ICP) 569 lipidomics in patient care 561–563 mitochondrial fatty acid β‐oxidation and organic acid metabolism 566–567 NAFLD/NASH 568–569 reference intervals and true values 564–565 reproducibility issue 563–564 trailblazing ceramides 559–561 vitamin D and its metabolites 558–559 vitamin D deficiency 570–571 coefficient of variation (CV) 266 collisionally activated dissociation (CAD) 183, 372 collision‐cross section (CCS) lipid identification and characterization with 166–168 for lipid structural analysis 168 measurements 129 collision‐induced dissociation (CID) 57, 136, 137, 171, 183–186, 190, 192–196, 200, 204–209, 232, 233, 235, 237, 242, 243, 249, 280, 297, 305, 307, 308, 310, 311, 340, 372, 399, 404, 407, 416, 429, 434, 437, 442–452, 455, 456, 518, 648, 690, 694, 696 compensation voltage (CV) 158, 165, 243 congenital adrenal hyperplasia (CAH) 567, 569–571 Coronavirus disease 2019 (COVID‐19) 627 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 706 covalent adduct chemical ionization (CACI) 369 crude lipid extracts bond types 43–44 fatty acids 44–45 lipid species and double bond series 45–46 in mammalian samples 42–43 C18‐sphingosine (C18‐So) 425, 437, 439, 441, 456 cyclic IMS (cIM) 157, 159–161 cyclic phosphatidic acid 417 cyclopropane fatty acids (CFAs) 207, 614 cytochrome P450 (CYP) 336–337, 440 d damage‐associated molecular patterns (DAMPs) 318 data analysis 3, 7, 10, 36, 78–79, 151, 172, 271, 276, 279, 280, 282, 535, 539, 541, 628, 634 data‐dependent acquisition (DDA) 135, 170–172, 228, 280, 696 deep structure determination 242–243 deisotoping procedure 92 dentate gyrus (DG) 459 deoxycholic acid (DCA) 510, 511, 569, 694 deoxydihydroceramides 436 deprotenization method 535 desorption electrospray ionisation (DESI) 126–127, 129, 132, 135, 137, 169 diacylglycerols (DGs) 363–364 electrospray ionization 365 dichloromethane (DCM) 20, 23, 27, 105, 488, 549 dicloromethane:methanol solvent 20 dietary lipids 571, 585, 596 differential ion mobility spectrometry (DIMS) 158, 243, 329, 330 differential mobility spectrometry (DMS) 158, 164, 169, 172, 203, 329, 374 diacylglycerol (DGs) 351, 357 dihydroceramides (DHCer) 427, 429, 435, 437, 439, 443, 536 dilution integrity 266, 268 dilution QC (dQC) 537 dimethylglycyl esters 492–493 4,4‐dimethyloxazoline (DMOX) 185, 295–296, 309, 354 direct infusion 27, 29, 41–82, 91, 186, 192, 201, 228, 518, 601–603, 648, 651 direct infusion MS workflows 50 DNA methylation 662–663 docosahexanoic acid (DHA) 45, 46, 330, 337, 339, 369, 588, 589, 591–594 double bond equivalents (DBEs) 47, 48 15dPGJ2 334 drift gas dopants and modifiers 163–164, 172 drift tube IMS (DTIMS) 151, 154–162, 164, 167, 169, 243 e eicosapentaenoic acid (EPA) 330, 337, 339, 369, 588, 589, 591–594 electron capture dissociation (ECD) 184 electron detachment dissociation (EDD) 184 electron impact excitation of ions from organics (EIEIO) 172, 202, 243, 374, 696 electron ionization 183, 230, 295, 646 electrospray ionization (ESI) 124, 195, 232, 365, 428 conventional 307 desorption 126–127 epoxidation 310 ion–ion chemistry 309–310 IR‐MALDESI 127 laser ablation 127 nanospray desorption 128 ozone‐induced dissociation 307–308 Paternò–Büchi reaction 308–309 silver ion liquid chromatography‐ESI 310 electrospray ionization (ESI‐MS) of lipid structure 41 707 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Index Index electrospray ionization tandem mass spectrometry 41, 57, 188, 328 epoxidation 194–195, 310, 696 equivalent carbon number (ECN) model 229, 246 essential fatty acids (EFAs) 588, 651 ethanolamine glycerophospholipid 405–417 ethanolamine lysoglycerophospholipids 408–409 external quality assurance (EQA) programs 565 f Fabry disease 450, 557, 567, 568 false discovery rates (FDR) 287 fatty acid methyl esters (FAME) 44, 91, 190, 192, 196, 354, 356, 357, 371, 589–591, 646 fatty acids (FA) 45, 233, 293, 646, 690–691 analysis 354–355 characterization 311 charge‐switch derivatization 186–187 classification 294–295 deuteration characterization 310–311 4,4‐dimethyloxazoline derivatization 295–296 electrospray ionization conventional 307 epoxidation 310 ion‐ion chemistry 309–310 ozone‐induced dissociation 307–308 Paternò–Büchi reaction 308–309 silver ion liquid chromatography‐ESI 310 gas chromatography 295–296 GC‐solvent mediated covalent adduct chemical ionization 296 branched chain FA 305 conjugated linoleic acids 304 double bond position assignment 296–304 quantitative analysis 305–307 liquid chromatography 295 picolinyl ester 296 structure 294 Fenton‐type chemistry 321 field asymmetric waveform ion mobility spectrometry (FAIMS) 129, 151, 158, 159, 161, 164, 165, 167, 169, 192, 243, 374 fish products 591, 592 F2‐isoprostane (F2‐IsoPs) 323, 337, 571 flame ionization detection (FID) 44, 354 flow injection analysis (FIA) 41, 53, 55, 91 flow injection analysis (FIA)‐MS/MS mode 536 Folch LLE method 24, 27 foodomics 377, 585, 586, 596 formalin fixation paraffin embedding (FFPE) 120 Fourier transform‐ion cyclotron resonance‐mass spectrometry (FT‐ICR‐MS) 122, 231 Fourier transform‐mass spectrometry (FT‐MS) 72, 75, 78, 82, 231, 244 fragmentation 4, 69, 73, 74, 78, 121, 124, 125, 151, 152, 161, 170–172, 183–185, 193, 194, 196, 197, 199–203, 207–209, 232–237, 240–243, 249, 257, 276–278, 293, 296, 298, 303, 304, 306, 309, 369, 372, 374, 397–417, 428, 437, 439, 441, 443, 445–447, 452, 456, 497, 516, 518, 519, 591, 608, 647, 693, 696 free fatty acids (FFA) 5, 18, 79, 124, 127, 130, 132, 133, 137, 195, 293, 362, 365, 371, 457, 458, 595, 609 functional foods 591, 596 g β‐galactosylceramide (GalCer) 446–449, 455 gangliosides 56, 125, 237, 240, 260, 425, 426, 450–456, 459, 661 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 708 gas chromatography (GC) 44, 230, 295 with flame ionization detection 354–355 gas chromatography mass spectrometry (GC‐MS) 228, 275, 295–296, 332, 334, 335, 337, 354, 356, 357, 362, 364, 487–488, 512, 516–518, 522, 589, 593, 601, 609, 646, 649 gas cluster ion beams (GCIBs) 125 Gaucher disease 446, 567, 568 genome‐wide association studies (GWASs) 540–541, 615 Girard reagents 493–496 Girard T reagent 129 glass homogenizer 21, 22 global quality control (gQC) sample 536, 538 β‐glucosylceramide (GlcCer) 446, 447, 457 acylglycerols 339, 340, 351, 596 glycerol 30, 47, 69, 136, 189, 207–210, 235–238, 351–353, 356, 366, 372, 374, 395–399, 401, 404, 406, 413, 610, 612, 644, 645, 691, 692 glycerolipids 5, 24, 29, 42, 47, 170, 172, 193, 207, 210, 242, 243, 260, 277, 278, 293, 294, 308, 351–380, 548 nomenclature 351 glycerophospholipid (GPL) 29, 659, 691–692 acyl phosphatidylglycerol 416–417 anionic lysoglycerophospholipids 416 bis(monoacylglycero) phosphate 413–414 building block pattern 397 cardiolipin 415–416 choline glycerophospholipid alkaline adducts 401, 404 protonated species 400–401 cyclic phosphatidic acid 417 diverse functions and structures of 395–397 ethanolamine glycerophospholipid 405–417 ethanolamine lysoglycerophospholipids 408–409 fragmentation patterns 400–417 molecular mechanisms 398–399 practical usage 399–400 recognition 397–398 N‐acyl phosphatidylethanolamine 416 N‐acyl phosphatidylserine 416 pattern recognition, building block pattern 397 phosphatidic acid 411 phosphatidylglycerol 412–413 phosphatidylinositol and polyphosphoinositides 409–411 phosphatidylserine 411–412 structures 44 glycosylinositol phosphorylceramides (GIPCs) 461, 607 Goslin 273, 280–282, 286 G protein‐coupled receptor (GPCR) 485, 690 h head group‐acylated lipids 611 Hedgehog (Hh) signaling pathway 485 hexosylceramides 137, 446–447 high‐performance liquid chromatography (HPLC) 91, 93, 98, 102, 227, 364, 433, 518, 519, 586, 593, 609, 642, 649 high resolution/accurate mass (HRAM) 41, 56, 61 high resolution demultiplexing (HRdm) 162, 163 high‐resolution mass spectrometers (HRMSs) 61, 63, 228 high resolution mass spectrometry (HRMS) 69, 81, 519, 538 lipid identification by 65–67 homogenization techniques bead mill 22 blender homogenizer 21 mortar and pestle 20–21 Potter‐Elvehjem apparatus 22 rotor–stator 21 709 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Index Index HUPO–PSI 274 hydrophilic interaction liquid chromatography (HILIC) 79, 92, 94–97, 99, 106, 107, 227, 229, 230, 365, 608, 651 i imaging mass spectrometry (IMS) of sphingolipids 458–459 infrared‐matrix‐assisted laser desorption‐ electrospray ionization (IR‐ MALDESI) 127, 129, 132, 137 infrared multiple photon dissociation (IRMPD) 184 inter/intrabatch effect 537 intrahepatic cholestasis of pregnancy (ICP) 569 ion–ion chemistry 309–310 ion mobility, of lipids 128–129 ion mobility spectrometry (IMS) 374 benefits for lipidomics 164–165 chemical space separation with 165–166 cyclic IMS (cIM) 159–160 data deconvolution software strategies 161–163 drift gas dopants and modifiers 163–164 drift tube IMS (DTIMS) 154–156 field asymmetric IMS (FAIMS) 158 in imaging and shotgun lipidomics 168–169 IMS‐MS/MS 169–172 lipid identification and characterization with 166–168 lipidomic identification 243 structure lossless ion manipulation (SLIM) 160–161 tandem IMS 161 techniques and platforms 154–158 trapped IMS (TIMS) 157–158 traveling wave ion mobility spectrometry (TWIMS) 156–157 iPF2α‐III 337 IsoalloLCA 694 isobaric lipid molecules 50, 81 isobaric mass 231 isomeric mass 231 isomers biological considerations of 329–331 challenges of 327–329 8‐iso‐PGF2α 337 isotope dilution analysis 327 isotopic correction type I 261–262 type II 262–263 k 3‐ketodihydrosphingosine reductase (KDSR) 429, 430, 436, 437, 461 3‐ketodihydrosphingosines (KDS) 427, 429 kit‐based metabolomics (Kit‐Met) 535, 536, 539, 540 l lactosylceramide (LacCer) 447, 449, 450, 455–457 laser ablation electrospray ionization (LAESI) 127, 135, 170 laser wavelength 121, 184 LC‐MS/MS analytical method 324–327 leukotrienes (LTs) 336, 588 limit of detection (LOD) 79, 161, 318, 326, 435, 489, 491, 538 limit of quantification (LOQ) 318, 326, 435, 492 limit of quantitation (LOQ) 266, 318 linear ion trap (LTQ) 244, 374 lipid class separation 7, 91–99, 106, 260, 262, 264, 550 lipid class specific fragments (LCF) 58 LipidCreator 273, 276–278, 286 lipid databases 285–286, 397, 635 lipid identification caveats/pitfalls 69–70 hierarchy 67, 69 by HRMS 65–67 for MSI in‐source fragmentation 133 ions generated by 132 isomer‐resolved 136–137 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 710 MS/MS development in 135 using accurate mass 133–135 by MS/MS 65 type‐II overlap 67–68 lipid ions 69, 183, 184, 189, 199, 210 LIPID MAPS nomenclature system 481 LIPID MAPS Structure Database (LMSD) 2, 9, 244, 449 lipid metabolism analysis 80–81 lipidomic analysis automation 31–34 clinical lipidomics identification and annotation 8–9 lipid ontology 10–11 liquid‐liquid extraction (LLE) 22–30 quantitation 9–10 reference materials and biological reference ranges 4–7 resuspension and solubilization 30–31 sample collection 17–19 sample origin 16–17 sampling and preanalytics tissue homogenization 19–22 lipidomic identification 227–228 chromatography 228–230 identification workflows 244, 249 ion mobility spectrometry 243–244 mass spectrometry 230–243 lipidomic profiling 533–534, 553 analytical platform 536 data acquisition 536–537 database creation 539–540 data processing 537–538 genome‐wide association studies (GWASs) 540–541 sample collection 534–535 sample preparation 535–541 lipidomic quantitation 255–256 chromatography MS 264–265 internal standards 257–261 isotopic correction 261–263 principle of 256–257 quality control (QC) 268 shotgun MS 263–264 validation 265–268 lipidomics 585 analysis 602 application 609 edible plants and vegetable oils 594–596 fish, shellfish and algae 591–594 in multi‐omics studies 627–630 classification 633 computational analysis methods 632 current challenges 635 data integration 632 planning and conducting 630–632 statistical integration 632 nutrition and human health 586–591 phosphatidic acids 601–604 phospholipase Ds 602 in plant science 615 profiling 545 workflow 228, 274–276 Lipidomics Informatics for Life‐Science (LIFS) 271, 272, 278 Lipidomics Standard Initiative (LSI) 3, 4, 9, 10, 42, 81, 272, 275, 278, 550, 552, 564, 630 lipid ontology 3, 10–11 lipid quantification calculation of concentration 76 internal standards 70–72 isotopic overlap 71–73, 76 species response 73–74, 77, 78 type‐I isotopic effect 71, 73 lipids cell biology 678–680 double and triple bonds 185–204 intracellular trafficking 674 early secretory pathway 676–678 endocytic pathway 674, 676 membrane biophysical properties 672–674 of organelles 669–674 ozone‐induced dissociation 187–192 structural analysis 168 of subcellular location 671–672 711 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Index Index LipidXplorer 78, 273, 279–281, 285, 286, 628, 629 lipopolysaccharide (LPS) 318 15‐lipoxygenating 321 liquid chromatography (LC) 9, 91–107, 152, 295, 399, 428, 610, 648, 651 liquid chromatography mass spectrometry (LC‐MS) 126, 243, 264, 272, 512, 518–519, 558, 627, 690 liquid chromatography–tandem mass spectrometry (LC‐MS/ MS) 323–325, 328–330, 334, 337, 339, 340, 488–498, 690, 692 liquid‐liquid extraction (LLE) 549 Alshehry method 29 Bligh and Dyer (BD) method 27 Butanol:Methanol (BUME) method 28–29 Folch LLE method 24, 27 Matyash/methyl‐tert‐butyl ether (mTBE) method 28 modified Folch and Bligh/Dyer (BD) methods 27–28 Rose and Oaklander (RO) method 28 three‐phase lipid extraction (3PLE) method 29–30 lithocholic acid (LCA) 510, 511, 694 LOC 326 locally weighted scatter plot smoothing (LOWESS) 537 lower limit of quantitation (LLOQ) 266, 326 LUX Score 273, 282–284 lxPostman 273, 280–282 lysophosphatidylcholines (LPC) 43, 55, 57, 91, 92, 536 lysophospholipids (LPLs) 4, 18, 194, 230, 535, 593 m MALDI‐2, 122, 128 MALDI‐MSI approach 136 Mason–Schamp equation 154 mass distribution vectors (MDVs) 643, 644, 649, 651 mass spectrometers (MS) 15, 41, 53, 184, 185, 205, 228, 257, 274, 279, 518, 550, 615 mass spectrometric analysis electrospray ionization of lipids 56 high‐resolution mass spectrometers (HRMSs) 61–64 multidimensional mass spectrometry 61, 63 tandem mass spectrometry 57–61 mass spectrometry (MS) 91, 151, 183, 271, 601, 609 additives 54–55 deep structure determination 242–243 direct infusion workflows 50 exact mass 230–232 fragment spectra 232–242 ionization 18 isobars and type‐II isotopic overlap 49, 52 isomers 48–49 lipid analysis and lipid concentration 54–55 lipid extraction 54 lipid structures analyzed by 46–48 preanalytics 50–54 sample derivatization 55 solvents 54–55 sphingolipids (SLs) 428 mass spectrometry imaging (MSI) 499 cell culture 119 of cholesterol and oxysterols in tissue 499, 500 electrospray ionisation 126–128 formalin fixation paraffin embedding 120 handling and storage 120 ion mobility 128–129 lipid identification for 132–137 matrix‐assisted laser desorption/ ionization 120–124 on‐tissue chemical derivatization 129–130 pre‐processing 119–120 quantification in 130–132 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 712 secondary ion mass spectrometry 124–126 sectioning and mounting 119 tissue samples 118 matrix‐assisted laser desorption/ ionization (MALDI) 2, 119–124, 127, 132, 133, 135, 137, 364, 428, 436, 440, 444, 447, 449, 452, 455, 458–460, 499, 614, 680 matrix‐assisted laser desorption ionization (MALDI)‐MS 125, 364 matrix‐assisted laser desorption/ ionization time‐of‐flight mass spectrometry (MALDI‐TOF/ MS) 689, 695 matrix associated laser desorption/ ionization (MALDI) 428 Matyash/methyl‐tert‐butyl ether (mTBE) method 28 mechanical shearing 21 metabolic age 662–664 metabolome genome‐wide association study (MGWAS) 540, 541 Metabolomics Standards Initiative (MSI) 275 methyl tert‐butyl ether (mTBE/ MTBE) 24, 28, 33, 54, 491, 549 minimally invasive diagnostic testing 568–569 mitochondrial fatty acid β‐oxidation 566–567 modified Folch and Bligh/Dyer (BD) methods 27–28 molecular fragmentation query language (MFQL) 78, 279, 280 molecular lipid fragments (MLF) 57, 60, 65, 69 monoacylglycerols (MAGs) 356 analysis 362 LC‐MS methods 357 softer ionization methods 357 monoacylglycerol (MGs) 351 monounsaturated fatty acid (MUFA) 294, 307, 428, 587, 588 mortar and pestle 20–21 MS technology 695–696 multi‐dimensional mass spectrometry‐ based shotgun lipidomics (MDMS‐SL) 61 multi‐omics 625 multiple precursor ion scans (MPIS) 57 multiple reaction monitoring (MRM) 260, 318, 324, 325, 369, 400, 437, 441, 443, 447, 456, 486, 489, 491–493, 497, 516, 521, 538, 559, 594 multi reaction monitoring (MRM) mode 431, 434, 435, 439, 449 n N‐acyl homoserine lactones (AHLs) 690, 691 N‐acyl phosphatidylethanolamine 416 N‐acyl phosphatidylserine 416 NAFLD/NASH 568–569 nanospray desorption electrospray ionization (nano‐DESI) 128 nanospray desorption electrospray ionization mass spectrometry 697 neurodegeneration 627, 662, 663, 673 neutral complex glycosphingolipids 447–450 neutral loss scans (NLS) 57, 63, 65, 81, 235, 369, 371, 397, 400, 647, 648 newborn screening (NBS) program 566, 567 nicotinic acid 490–492 15 N‐labelled sphingolipids 126 non‐alcoholic fatty liver disease (NAFLD) 377, 511, 512, 557, 568–569 nonaqueous reversed‐phase liquid chromatography (NARP‐ HPLC) 102–103, 105, 368, 596 non‐esterified fatty acids (NEFA) 293 non‐polar lipids 488, 658 normal‐phase liquid chromatography 94–95, 450, 592 713 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Index Index o 1‐O‐acylceramides 427, 441–443 obstetric cholestasis (OC) 569 octadecylsilyl 536 olive oil 366, 372, 587, 594, 595 omega‐3 541, 588–593 omega‐6 541, 588–591, 594, 596 omics 2, 8, 78, 255, 260, 274, 275, 282, 585, 625, 626, 630–633, 635, 676, 678–680 on‐tissue chemical derivatization (OTCD) 129–130 Orbitrap 2, 41, 56, 61, 67, 72, 133, 135, 191, 227, 228, 231, 233, 244, 264, 454, 500, 519, 650, 651 organellar identity 672, 675 organic acid metabolism 566–567 oxidative stress, markers of 562, 563, 571 oxidized PL (oxPL) 322, 339, 340 oxygen attachment dissociation (OAD) 696 oxylipins 205, 233–234 experimental system, focusing on plasma and serum 321–322 handling plasma 322–323 LC‐MS/MS analytical method 324–327 to phospholipids 339–340 plasma extraction from 323–324 quality assessment and control 327 sample collection preparation and storage 321 urine metabolites 331–339 oxysterols 485 in blood plasma and serum 486 classical GC‐MS Methods 487–488 LC‐MS/MS analysis 488–489 mass spectrometry imaging (MSI) 499, 500 ozone‐induced dissociation (OzID) 9, 47, 136, 185, 188–192, 209, 242, 243, 248, 249, 307–308, 310, 375, 696 p parallel accumulation–serial fragmentation (PASEF) 161 partial equilibration 95 Paternò–Büchi (PB) reactions 136, 192–194, 199, 296, 308–309, 375, 446, 696 pathogen‐associated molecular patterns (PAMPs) 318 PGD2 334–336, 339 PGE2 317, 318, 322, 329, 330, 332, 334, 335, 339, 340 PGJ2 334 phosphatidic acids (PA) 18, 56, 133, 201, 235–237, 246, 260, 264, 396, 404, 406, 411–413, 415, 601–606, 641, 647, 691 phosphatidylcholines (PC) 5, 42, 43, 55, 91, 92, 128, 190–192, 200, 201, 203, 204, 208–210, 229, 260, 401, 444–446, 536, 548, 560, 595, 601, 629, 645, 670, 691 hierarchical annotation of 47 phosphatidylethanolamine (PE) 42, 43, 118, 119, 191, 205, 231, 260, 592, 595, 601, 645, 670, 691 lipid species of 46 phosphatidylglycerol (PG) 6, 55, 164, 235, 261, 412, 601, 647, 691 phosphatidylinositol and polyphosphoinositides 409–410 phosphatidylserine (PS) 42, 43, 118, 119, 261, 411–412, 592, 645, 670, 691, 696 phospholipase A (PLA) 18 phospholipase D (PLD) 18, 443, 602–604 phospholipids (PL) 234, 237, 322, 647 in flowering and diurnal metabolism 604–606 oxylipins to 339–340 phosphorus 602, 603, 608, 609 phosphorylated sphingoid bases 433–436 photodissociation 184, 187, 199–202, 204, 206 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 714 picolinic acid 242, 490, 491 picolinyl ester 296, 355 plasma analysis 79–80 plasmalogens 44, 48, 191, 231, 661, 673, 692 polyphosphoinositides (PPIs) 55, 56, 410 polyunsaturated fatty acids (PUFAs) 17, 127, 195, 201, 294, 317, 320, 323, 337, 369, 541, 561, 588, 590, 593, 594, 612 post‐ionization approaches 122, 129 Potter–Elvenhjem apparatus 20, 22 precursor ion scans (PIS) 57, 61, 63, 65, 71, 81, 186, 260, 397, 400, 647 principal component analysis (PCA) 283, 628 prostacyclin 318, 335–336 prostaglandins (PGs) 2, 128, 132, 317, 318, 321, 332–339, 365, 588, 691, 692 prostanoids/prostaglandins (PG) 317 PSI‐MS 274 push–pull‐protect approach 614 q quadrupole time‐of‐flight mass spectrometer (QTOF) 41, 57, 63, 191, 202, 203, 604–605 qualification phase 546 quality assessment and control 327 quality control (QC) 268, 287 validation and 550–551 quantitation error 551 quantitative‐MSI (Q‐MSI) 130, 132 quorum sensing 690 r rate of autoxidation 18 recrystallization methods 121 reference intervals 564, 565 reference measurement procedure (RMP) 565 regioisomers 99, 105, 164, 208, 210, 243, 337, 353, 354, 367, 372, 398, 399, 401, 403, 407–409, 411, 413, 415, 416, 596 relative standard deviation (RSD) 156, 266, 551 reproducibility issue 563–564 resuspension, lipidomic analysis 30–31 reversed‐phase (RP) 264, 328, 329 chromatography 92, 328, 433 reversed phase HPLC 228–230, 364, 437, 519 reversed‐phase liquid chromatography 9, 99–101 reversed‐phase liquid chromatography electrospray ionization triple quadrupole mass spectrometry 606 ring oxysterols 485 Rose and Oaklander (RO) method 28 rotor–stator 21 s saccharolipids 42, 351, 586, 694–695 saturated fatty acids (SFAs) 186, 195, 587, 594 secondary ion mass spectrometry (SIMS) 119, 124–126, 133, 458, 680 selected reaction monitoring (SRM) methods 234 shellfish 591 shotgun lipidomics 42, 56, 78, 82, 133, 151, 168, 169, 191, 244, 272, 273, 279, 285, 371, 377, 400, 405, 410, 439, 564, 630 shotgun MS 260, 262–264, 279 signal‐to‐noise (S/N) ratio 158, 165, 169, 172, 326, 635 silver ion chromatography 103–105, 353 simplified molecular‐input line‐entry system (SMILES) format 283 SIMS‐MSI 126, 133 single nucleotide polymorphisms (SNPs) 540–541 skin omega‐hydroxy ceramides 440–441 Skyline 276, 278 solid‐phase extraction (SPE) 32 solubilization, lipidomic analysis 30–31 specialist pro‐resolving mediators (SPM) 325, 330 715 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Index Index specialist resolving mediators 324 sphingoid bases 425, 429, 433 phosphorylated 433–436 sphingolipids (SLs) 237, 241, 606, 693 biosynthesis pathways 460 imaging mass spectrometry (IMS) of 458–460 mass spectrometry 428 nomenclature 426–428 phosphorylated sphingoid bases 433–436 sphingoid bases 425, 429, 433 in vertebrates 429–456 sphingomyelins (SM) 231, 444, 446 stable heavy isotopes 642 stable isotope labeling 456, 458 sterol lipids (SL) 481 analytical challenges 486 in blood plasma and serum 486 in cells 483–484 classical GC‐MS methods 487–488 LC‐MS/MS analysis 488–489 dimethylglycyl esters 492–493 Girard hydrazine reagents 493–497 nicotinyl esters 491–492 4‐phenyl‐1,2,4‐triazoline‐3,5‐ dione 497 picolinyl esters 490–491 structure 482 sterols 29, 30, 36, 94, 129, 242, 482, 483, 485–491, 495–497, 501, 563, 586, 670, 679 steryl esters 500 structural heterogeneity 293 structure lossless ion manipulation (SLIM) 160–161, 167, 169, 172 sulfatides 126, 425, 426, 455–456, 459 supercritical fluid chromatography (SFC) 91, 97, 99, 366, 435, 512, 519 surface‐induced dissociation (SID) 184 syringe pump 55 t tandem IMS 160, 161 tandem mass spectrometry 48, 56, 65, 198, 428, 431, 439, 447, 449, 450, 455 targeted lipidomics 272, 273, 276, 278, 690 thaw mounting techniques 119 three‐phase lipid extraction (3PLE) method 24, 29–30 thromboxane 335–336 time‐aligned parallel (TAP) fragmentation 171, 172 time‐of‐flight (TOF) 61, 124, 152, 364, 519 analyzer 49, 133 tissue homogenization 20, 21 tissues analysis 80 toll‐like receptor (TLR4) 695 total ion chromatogram (TIC) 245, 520 total ion current (TIC) spectrum 244, 245 tracer lipidomics 642 experimental conditions 644–645 fatty acids 646–647 flux analysis 642–644 isotopic effects 649–651 lipidome‐wide tracer analysis 649–653 MS/MS analysis 652–653 phospholipids 647–649 stable heavy isotopes 642 tracer metabolomics 645, 653 transition or inclusion list 276 trapped‐ion mobility spectrometry (TIMS) 128, 151, 157–159, 161, 167, 171, 194, 243 traveling wave ion mobility spectrometry (TWIMS) 129, 151, 156–160, 169, 171, 243, 374 triacylglycerols (TAGs) 91, 229, 366, 368–369, 611 covalent adduct chemical ionization 369 ion mobility MS 374–375 lipidomic 375–379 Oz‐ID for 375 Paternò–Büchi reactions 375 quantification 367–369 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License 716 structural information 366–367 triacylglycerol (TGs) 16, 42, 73, 91, 308, 351, 510, 522, 535, 565, 568, 586, 587, 593–596, 611, 627, 661 triple quadrupole MS (QqQ) 55–57, 62, 63, 67, 69, 72, 82, 324, 592, 593 type‐I isotopic effect 71, 73 type‐II isotopic overlap 50, 51 type‐II overlap, lipid identification 67–68 u ultrahigh‐performance liquid chromatography (UHPLC) 93, 97, 98, 191, 371 ultrahigh‐performance liquid chromatography (UHPLC)/ MS 97–100, 106, 264, 550, 552, 553 ultrahigh‐performance liquid chromatography triple quadrupole mass spectrometry (UHPLC‐MS/ MS) method 535, 536 ultrahigh‐performance supercritical fluid chromatography (UHPSFC) 92–94, 97, 99 ultraviolet photodissociation (UVPD) 137, 184, 199–201, 204, 206–208, 243, 249, 452, 696 unsaturated lipids electron‐induced dissociation of 202–204 photodissociation of 199–202 upper limit of quantitation (ULOQ) 266 urine oxylipin metabolites 331–339 UV light 189, 194, 199, 200, 243, 570 v vegetables 594, 595 vitamin D deficiency 570–571 and its metabolites 558–559 w whole‐genome sequence datasets 541 widely targeted metabolomics (WT‐Met) analysis 536, 538 717 Downloaded from https://onlinelibrary.wiley.com/doi/ by THU VIEN - Fiji - Hinari access , Wiley Online Library on [30/03/2023] See the Terms and Conditions (https://onlinelibrary.wiley.com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License Index