Liquid Chromatography-Mass Spectrometry (LC-MS)-Based Lipidomics for Studies of Body Fluids and Tissues

Molecular Biology of the Cell

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A comprehensive classification system for lipids

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The emerging field of lipidomics

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Large-Scale Human Metabolomics Studies: A Strategy for Data (Pre-) Processing and Validation

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MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data

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Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes

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Processing methods for differential analysis of LC/MS profile data

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Assessing the Nature of Lipid Raft Membranes

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Nonlinear Data Alignment for UPLC−MS and HPLC−MS Based Metabolomics: Quantitative Analysis of Endogenous and Exogenous Metabolites in Human Serum

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Human gut microbes impact host serum metabolome and insulin sensitivity

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The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

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Comprehensive analysis of lipids in biological systems by liquid chromatography-mass spectrometry

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Metabolomics: A Primer

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Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease

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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

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Metabolome in progression to Alzheimer's disease

Orešič, M., Hyötyläinen, T., Herukka, S.-K., Sysi‐Aho, M., Mattila, I. M., Seppänan-Laakso, T., Julkunen, V., Gopalacharyulu, P. V., Hallikainen, M., Koikkalainen, J. R., et al. (2011) · Translational Psychiatry · doi:10.1038/tp.2011.55 · Cited by 283

Ultra Performance Liquid Chromatography and High Resolution Mass Spectrometry for the Analysis of Plant Lipids

Hummel, J., Segu, S., Li, Y., Irgang, S., Jüppner, J., & Giavalisco, P. (2011) · Frontiers in Plant Science · doi:10.3389/fpls.2011.00054 · Cited by 221

Statistical Methods for Handling Unwanted Variation in Metabolomics Data

Livera, A. M. D., Sysi‐Aho, M., Jacob, L., Gagnon-Bartsch, J. A., Castillo, S., Simpson, J. A., & Speed, T. P. (2015) · Analytical Chemistry · doi:10.1021/ac502439y · Cited by 195

Mammalian cell metabolomics: Experimental design and sample preparation

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Lipidomics: Potential role in risk prediction and therapeutic monitoring for diabetes and cardiovascular disease

Meikle, P. J., Wong, G., Barlow, C. K., & Kingwell, B. A. (2014) · Pharmacology & Therapeutics · doi:10.1016/j.pharmthera.2014.02.001 · Cited by 189

Role of liquid chromatography–high-resolution mass spectrometry (LC-HR/MS) in clinical toxicology

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Accurate Quantification of Lipid Species by Electrospray Ionization Mass Spectrometry — Meets a Key Challenge in Lipidomics

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Mass Spectrometry Based Lipidomics: An Overview of Technological Platforms

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Prediction of non-alcoholic fatty-liver disease and liver fat content by serum molecular lipids

Orešič, M., Hyötyläinen, T., Kotronen, A., Gopalacharyulu, P. V., Nygrén, H., Arola, J. T., Castillo, S., Mattila, I. M., Hakkarainen, A., Borra, R., et al. (2013) · Diabetologia · doi:10.1007/s00125-013-2981-2 · Cited by 173

Phospholipids and insulin resistance in psychosis: A lipidomics study of twin pairs discordant for schizophrenia

Orešič, M., Seppänen‐Laakso, T., Sun, D., Tang, J. P., Therman, S., Viehman, R., Mustonen, U., van Erp, T. G., Hyötyläinen, T., Thompson, P. M., et al. (2012) · eScholarship (California Digital Library) · Cited by 168

Human Tear Fluid Lipidome: From Composition to Function

Rantamäki, A. H., Seppänen‐Laakso, T., Orešič, M., Jauhiainen, M., & Holopainen, J. M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019553 · Cited by 151

Lipidome as a predictive tool in progression to type 2 diabetes in Finnish men

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Integration of molecular profiles in a longitudinal wellness profiling cohort

Tebani, A., Gummesson, A., Zhong, W., Schuppe‐Koistinen, I., Lakshmikanth, T., Olsson, L. M., Boulund, F., Neiman, M., Stenlund, H. C., Hellström, C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-18148-7 · Cited by 156

Sphingolipids as prognostic biomarkers of neurodegeneration, neuroinflammation, and psychiatric diseases and their emerging role in lipidomic investigation methods

van Kruining, D., Luo, Q., van Echten‐Deckert, G., Mielke, M. M., Bowman, A. P., Ellis, S. R., Oliveira, T. G., & Martínez‐Martínez, P. (2020) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2020.04.009 · Cited by 138

Lipidomics Applications for Discovering Biomarkers of Diseases in Clinical Chemistry

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Prolonged sleep restriction induces changes in pathways involved in cholesterol metabolism and inflammatory responses

Aho, V., Ollila, H. M., Kronholm, E., Bondia-Pons, I., Soininen, P., Kangas, A. J., Hilvo, M., Seppälä, I., Kettunen, J., Oikonen, M., et al. (2016) · Scientific Reports · doi:10.1038/srep24828 · Cited by 126

A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links

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Circulating triacylglycerol signatures and insulin sensitivity in NAFLD associated with the E167K variant in TM6SF2

Zhou, Y., Llauradó, G., Orešič, M., Hyötyläinen, T., Orho‐Melander, M., & Yki‐Järvinen, H. (2014) · Journal of Hepatology · doi:10.1016/j.jhep.2014.10.010 · Cited by 112

Effects of ellagitannin‐rich berries on blood lipids, gut microbiota, and urolithin production in human subjects with symptoms of metabolic syndrome

Puupponen‐Pimiä, R., Seppänen‐Laakso, T., Kankainen, M., Maukonen, J., Törrönen, R., Kolehmainen, M., Leppänen, T., Moilanen, E., Nohynek, L. J., Aura, A., et al. (2013) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201300280 · Cited by 109

A reversed-phase capillary ultra-performance liquid chromatography–mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling

Gao, X., Zhang, Q., Meng, D., Isaac, G., Zhao, R., Fillmore, T., Chu, R., Zhou, J., Tang, K., Hu, Z., et al. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-5773-5 · Cited by 99

Decreased Cord-Blood Phospholipids in Young Age–at–Onset Type 1 Diabetes

Torre, D. L., Seppänen‐Laakso, T., Larsson, H. E., Hyötyläinen, T., Ivarsson, S. A., Lernmark, Å., Orešič, M., & and the DiPiS Study Group (2013) · Diabetes · doi:10.2337/db13-0215 · Cited by 97

Lipidomics in Ulcerative Colitis Reveal Alteration in Mucosal Lipid Composition Associated With the Disease State

Diab, J., Hansen, T., Goll, R., Stenlund, H. C., Ahnlund, M., Jensen, E., Möritz, T., Florholmen, J., & Forsdahl, G. (2019) · Inflammatory Bowel Diseases · doi:10.1093/ibd/izz098 · Cited by 95

Opportunities and Challenges for Machine Learning in Rare Diseases

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Interaction between dietary lipids and gut microbiota regulates hepatic cholesterol metabolism

Caesar, R., Nygrén, H., Orešič, M., & Bäckhed, F. (2016) · Journal of Lipid Research · doi:10.1194/jlr.m065847 · Cited by 94

Optimizing the lipidomics workflow for clinical studies—practical considerations

Hyötyläinen, T., & Orešič, M. (2015) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-015-8633-2 · Cited by 94

Metabolic Regulation in Progression to Autoimmune Diabetes

Sysi‐Aho, M., Ermolov, A., Gopalacharyulu, P. V., Tripathi, A., Seppänen‐Laakso, T., Maukonen, J., Mattila, I. M., Ruohonen, S. T., Vähätalo, L. H., Yetukuri, L., et al. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002257 · Cited by 91

Cord Serum Lipidome in Prediction of Islet Autoimmunity and Type 1 Diabetes

Orešič, M., Gopalacharyulu, P. V., Mykkänen, J., Lietzén, N., Mäkinen, M., Nygrén, H., Simell, S., Simell, V., Hyöty, H., Veijola, R., et al. (2013) · Diabetes · doi:10.2337/db13-0159 · Cited by 89

Differential Intrahepatic Phospholipid Zonation in Simple Steatosis and Nonalcoholic Steatohepatitis

Wattacheril, J. J., Seeley, E. H., Angel, P. M., Chen, H., Bowen, B. P., Lanciault, C., Caprioli, R. M., Abumrad, N. N., & Flynn, C. R. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057165 · Cited by 88

Systems biology strategies to study lipidomes in health and disease

Hyötyläinen, T., & Orešič, M. (2014) · Progress in Lipid Research · doi:10.1016/j.plipres.2014.06.001 · Cited by 83

Integration of Metabolomics and Expression of Glycerol-3-phosphate Acyltransferase (GPAM) in Breast Cancer—Link to Patient Survival, Hormone Receptor Status, and Metabolic Profiling

Brockmöller, S. F., Bucher, E., Müller, B. M., Budczies, J., Hilvo, M., Griffin, J. L., Orešič, M., Kallioniemi, O., Iljin, K., Loibl, S., et al. (2011) · Journal of Proteome Research · doi:10.1021/pr200685r · Cited by 77

Exercise training improves mitochondrial respiration and is associated with an altered intramuscular phospholipid signature in women with obesity

Mendham, A. E., Goedecke, J. H., Zeng, Y., Larsen, S., George, C., Hauksson, J. B., Smidt, M. F.-D., Chibalin, A., Olsson, T., & Chorell, E. (2021) · Diabetologia · doi:10.1007/s00125-021-05430-6 · Cited by 73

Lipidomics in nutrition and food research

Hyötyläinen, T., Bondia‐Pons, I., & Orešič, M. (2013) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201200759 · Cited by 70

Prenatal exposure to perfluoroalkyl substances modulates neonatal serum phospholipids, increasing risk of type 1 diabetes

McGlinchey, A., Sinioja, T., Lamichhane, S., Sen, P., Bodin, J., Siljander, H., Dickens, A. M., Geng, D., Carlsson, C., Duberg, D., et al. (2020) · Environment International · doi:10.1016/j.envint.2020.105935 · Cited by 61

Circulating Triacylglycerol Signatures in Nonalcoholic Fatty Liver Disease Associated With the I148M Variant in PNPLA3 and With Obesity

Hyysalo, J., Gopalacharyulu, P. V., Bian, H., Hyötyläinen, T., Leivonen, M., Jaser, N., Juuti, A., Honka, M., Nuutila, P., Olkkonen, V. M., et al. (2013) · Diabetes · doi:10.2337/db13-0774 · Cited by 63

PGC-1α Coordinates Mitochondrial Respiratory Capacity and Muscular Fatty Acid Uptake via Regulation of VEGF-B

Mehlem, A., Palombo, I., Wang, X., Hagberg, C. E., Eriksson, U., & Falkevall, A. (2016) · Diabetes · doi:10.2337/db15-1231 · Cited by 60

Novel Approach for Analysis of Bronchoalveolar Lavage Fluid (BALF) Using HPLC-QTOF-MS-Based Lipidomics: Lipid Levels in Asthmatics and Corticosteroid-Treated Asthmatic Patients

Kang, Y. P., Lee, W. J., Hong, J. Y., Lee, S. B., Park, J. H., Kim, D., Park, S., Park, C., Park, H., & Kwon, S. W. (2014) · Journal of Proteome Research · doi:10.1021/pr5002059 · Cited by 59

Metabolic Signatures of the Exposome—Quantifying the Impact of Exposure to Environmental Chemicals on Human Health

Orešič, M., McGlinchey, A. J., Wheelock, C. E., & Hyötyläinen, T. (2020) · Metabolites · doi:10.3390/metabo10110454 · Cited by 52

Plasma Biomarkers for Alzheimer’s Disease: Much Needed But Tough to Find

Bazenet, C. E., & Lovestone, S. (2012) · Biomarkers in Medicine · doi:10.2217/bmm.12.48 · Cited by 48

Three‐dimensional genetic networks among seed oil‐related traits, metabolites and genes reveal the genetic foundations of oil synthesis in soybean

Liu, J., Li, P., Zhang, Y., Guo, L., Li, G., Han, X., Dunwell, J. M., & Zhang, Y. (2020) · The Plant Journal · doi:10.1111/tpj.14788 · Cited by 48

The state of the art in plant lipidomics

Kehelpannala, C., Rupasinghe, T., Hennessy, T., Bradley, D. A., Ebert, B., & Roessner, U. (2021) · Molecular Omics · doi:10.1039/d1mo00196e · Cited by 47

Influence of sample preparation on lipidomics analysis of polar lipids in adipose tissue

López-Bascón, M. A., Calderón-Santiago, M., Sánchez-Ceinos, J., Fernández-Vega, A., Guzmán‐Ruiz, R., López‐Miranda, J., Malagón, M. M., & Priego‐Capote, F. (2017) · Talanta · doi:10.1016/j.talanta.2017.09.017 · Cited by 47

DGAT1 activity synchronises with mitophagy to protect cells from metabolic rewiring by iron depletion

Long, M., Sánchez-Martínez, Á., Longo, M., Suomi, F., Stenlund, H. C., Johansson, A. I., Ehsan, H., Salo, V. T., Montava‐Garriga, L., Naddafi, S., et al. (2022) · The EMBO Journal · doi:10.15252/embj.2021109390 · Cited by 48

Serum, plasma and erythrocyte membrane lipidomes in infants fed formula supplemented with bovine milk fat globule membranes

Grip, T., Dyrlund, T. S., Ahonen, L. L., Domellöf, M., Hernell, O., Hyötyläinen, T., Knip, M., Lönnerdal, B. L., Orešič, M., & Timby, N. (2018) · Pediatric Research · doi:10.1038/s41390-018-0130-9 · Cited by 46

Metabolome and fecal microbiota in monozygotic twin pairs discordant for weight: a Big Mac challenge

Bondia‐Pons, I., Maukonen, J., Mattila, I. M., Rissanen, A., Saarela, M., Kaprio, J. A., Hakkarainen, A., Lundbom, J., Lundbom, N. M. I., Hyötyläinen, T., et al. (2014) · The FASEB Journal · doi:10.1096/fj.14-250167 · Cited by 46

Integrated LC/MS-based lipidomics and transcriptomics analyses revealed lipid composition heterogeneity between pectoralis intramuscular fat and abdominal fat and its regulatory mechanism in chicken

Wang, D., Qin, P., Zhang, K., Wang, Y., Guo, Y., Cheng, Z., Li, Z., Tian, Y., Kang, X., Li, H., et al. (2023) · Food Research International · doi:10.1016/j.foodres.2023.113083 · Cited by 44

Analytical approaches for lipidomics and its potential applications in neuropsychiatric disorders

Sethi, S., Hayashi, M. A. F., Sussulini, A., Tasić, L., & Brietzke, E. M. (2015) · The World Journal of Biological Psychiatry · doi:10.3109/15622975.2015.1117656 · Cited by 46

The Gut Microbiota Modulates Glycaemic Control and Serum Metabolite Profiles in Non-Obese Diabetic Mice

Greiner, T. U., Hyötyläinen, T., Knip, M., Bäckhed, F., & Orešič, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110359 · Cited by 44

Extending metabolome coverage for untargeted metabolite profiling of adherent cultured hepatic cells

García‐Cañaveras, J. C., López, S. A., Castell, J. V., Donato, M. T., & Lahoz, A. (2016) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-015-9227-8 · Cited by 47

Evaluation of Extraction Protocols for Simultaneous Polar and Non-Polar Yeast Metabolite Analysis Using Multivariate Projection Methods

Tambellini, N. P., Zaremberg, V., Turner, R. J., & Weljie, A. M. (2013) · Metabolites · doi:10.3390/metabo3030592 · Cited by 42

Changes in the Lipidomic Profile of Aqueous Humor in Open-Angle Glaucoma

Cabrerizo, J., Urcola, A., & Vecino, E. (2017) · Journal of Glaucoma · doi:10.1097/ijg.0000000000000603 · Cited by 42

Uncovering Structural Diversity of Unsaturated Fatty Acyls in Cholesteryl Esters via Photochemical Reaction and Tandem Mass Spectrometry

Ren, J., Franklin, E. T., & Xia, Y. (2017) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-017-1639-6 · Cited by 43

Comparative Nontargeted Profiling of Metabolic Changes in Tissues and Biofluids in High-Fat Diet-Fed Ossabaw Pig

Hanhineva, K., Barri, T., Kolehmainen, M., Pekkinen, J., Pihlajamäki, J., Vesterbacka, A., Solano-Aguilar, G. I., Mykkänen, H. M., Dragsted, L. O., Urban, J. F., et al. (2013) · Journal of Proteome Research · doi:10.1021/pr400257d · Cited by 41

Concentrations of Purine Metabolites Are Elevated in Fluids from Adults and Infants and in Livers from Mice Fed Diets Depleted of Bovine Milk Exosomes and their RNA Cargos

Aguilar-Lozano, A., Baier, S. R., Grove, R. A., Shu, J., Giraud, D., Leiferman, A., Mercer, K. E., Cui, J., Badger, T. M., Adamec, J., et al. (2018) · Journal of Nutrition · doi:10.1093/jn/nxy223 · Cited by 39

A Phospholipid Profile at 4 Months Predicts the Onset of Celiac Disease in at-Risk Infants

Auricchio, R., Galatola, M., Cielo, D., Amoresano, A., Caterino, M., Vita, E. D., Illiano, A., Troncone, R., Greco, L., & Ruoppolo, M. (2019) · Scientific Reports · doi:10.1038/s41598-019-50735-7 · Cited by 39

Serum metabolite profile associates with the development of metabolic co-morbidities in first-episode psychosis

Suvitaival, T., Mantere, O., Kieseppä, T., Mattila, I. M., Pöhö, P., Hyötyläinen, T., Suvisaari, J., & Orešič, M. (2016) · Translational Psychiatry · doi:10.1038/tp.2016.222 · Cited by 40

Berberine Could Ameliorate Cardiac Dysfunction via Interfering Myocardial Lipidomic Profiles in the Rat Model of Diabetic Cardiomyopathy

Dong, S., Zhang, S., Chen, Z., Zhang, R., Tian, L., Cheng, L., Shang, F., & Sun, J. (2018) · Frontiers in Physiology · doi:10.3389/fphys.2018.01042 · Cited by 37

Scoparone affects lipid metabolism in primary hepatocytes using lipidomics

Zhang, A., Qiu, S., Sun, H. J., Zhang, T., Guan, Y., Han, Y., Yan, G., & Wang, X. (2016) · Scientific Reports · doi:10.1038/srep28031 · Cited by 36

Optimization of metabolite extraction of human vein tissue for ultra performance liquid chromatography-mass spectrometry and nuclear magnetic resonance-based untargeted metabolic profiling

Anwar, M. A., Vorkas, P. A., Li, J. V., Shalhoub, J., Want, E. J., Davies, A. H., & Holmes, E. C. (2015) · The Analyst · doi:10.1039/c5an01041a · Cited by 35

Effects of a Lacto-Ovo-Vegetarian Diet on the Plasma Lipidome and Its Association with Atherosclerotic Burden in Patients with Coronary Artery Disease—A Randomized, Open-Label, Cross-over Study

Djekic, D., Shi, L. S., Calais, F., Carlsson, F., Landberg, R., Hyötyläinen, T., & Fröbert, O. (2020) · Nutrients · doi:10.3390/nu12113586 · Cited by 35

The Influence of Sample Collection Methodology and Sample Preprocessing on The Blood Metabolic Profile

Jørgenrud, B., Jäntti, S. E., Mattila, I. M., Pöhö, P., Rnningen, K. S., Yki‐Järvinen, H., Orešič, M., & Hyötyläinen, T. (2015) · Bioanalysis · doi:10.4155/bio.15.16 · Cited by 35

Combined extraction of acyl carnitines and 26:0 lysophosphatidylcholine from dried blood spots: Prospective newborn screening for X-linked adrenoleukodystrophy

Sandlers, Y., Moser, A. B., Hubbard, W. C., Kratz, L. E., Jones, R. O., & Raymond, G. V. (2012) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2011.11.195 · Cited by 38

NMR- and MS-based metabolomics: various organ responses following naphthalene intervention

Ling, Y. S., Liang, H., Chung, M.-H., Lin, M.-H., & Lin, C. (2014) · Molecular BioSystems · doi:10.1039/c4mb00090k · Cited by 33

Prepartal dietary energy alters transcriptional adaptations of the liver and subcutaneous adipose tissue of dairy cows during the transition period

Selim, S., Salin, S., Taponen, J., Vanhatalo, A., Kokkonen, T., & Elo, K. (2014) · Physiological Genomics · doi:10.1152/physiolgenomics.00115.2013 · Cited by 33

Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter‐like lipids

Bergenholm, D., Gossing, M., Wei, Y., Siewers, V., & Nielsen, J. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26518 · Cited by 33

Ultraperformance convergence chromatography‐high resolution tandem mass spectrometry for lipid biomarker profiling and identification

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Isoenergetic diets differing in their n‐3 fatty acid and polyphenol content reflect different plasma and HDL‐fraction lipidomic profiles in subjects at high cardiovascular risk

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