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Lipidomics

Lipidomics is the study of the structure and function of the complete set of lipids (the lipidome) produced in a cell, organism, or biological material and their interactions with other biomolecules. At EMSL, our lipidomics platform specializes in complex lipids such as phospholipids, glycerolipids, and sphingolipids. Specifically, we analyze lipid extracts using liquid chromatography tandem mass spectrometry (LC-MS/MS), which enables us to identify the type of lipids present and their associated acyl chains. Currently, our database contains over 45,000 lipids and is customizable to meet users’ needs.

Research application

Available instruments

Tips for success

  • Make sure your study is designed to answer your scientific questions. This includes appropriate controls, biological replicates, and statistical power.
  • As lipids are sensitive to degradation, biological samples should be flash frozen immediately after sampling and stored at -80°C.
  • Avoid plastic, especially those that may leave a residue on the samples. Lipids are extracted from biological samples using organic solvents (e.g., methanol and chloroform), which also dissolve most types of plastics. Plasticizers are common contaminants, and their presence could limit or decrease the number of lipids that can be identified. This can result in an incomplete and inaccurate profile of the lipidome. This is a common problem for samples that have a low amount of total lipids (please see below tip on small samples amounts).
  • Glass vials can also leave a reside. Pre-wash glassware with methanol and/or chloroform to minimize contamination.
  • For samples that are limited in size, ship your samples in containers that can also be used for extracting the lipids. This will minimize the number of times samples are transferred and, therefore, sample loss.

Contributing team and resources

EMSL develops and deploys capabilities for the user program by conducting original research independently or in partnership with others and by adapting/advancing science and technologies developed outside of EMSL. In some instances, EMSL directly deploys mature capabilities developed by others where there is value for the EMSL user community. The following grants/activities, PI’s and teams contributed to the development of this capability: 

  • Tom Metz and Jennifer Kyle, NIH NIDDK grants DK070146 and DK071283, NIH NIAID contract HHSN272200800060C and awards U54AI081680 and U19AI106772, DOE Low Dose Radiation Program and BER Genomics Science Program.

Related publications

  • Ding J, Sorensen CM, Jaitly N, Jiang H, Orton DJ, Monroe ME, Moore RJ, Smith RD, Metz TO. 2008. "Application of the accurate mass and time tag approach in studies of the human blood lipidome." J Chromatogr B Analyt Technol Biomed Life Sci. 871(2):243-52. doi: 10.1016/j.jchromb.2008.04.040
  • Gao X, Zhang Q, Meng D, Isaac G, Zhao R, Fillmore TL, Chu RK, Zhou J, Tang K, Hu Z, Moore RJ, Smith RD, Katze MG, Metz TO. 2012. "A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling." Anal Bioanal Chem. 402(9):2923-33. doi: 10.1007/s00216-012-5773-5
  • Kyle JE, Crowell KL, Casey CP, Fujimoto GM, Kim S, Dautel SE, Smith RD, Payne SH, Metz TO. 2017. "LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data." Bioinformatics. 33 (11):1744-1746. doi: 10.1093/bioinformatics/btx046

 

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