Lipidomics

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Study of complete lipid profile in organisms

title: "Lipidomics" type: doc version: 1 created: 2026-02-28 author: "Wikipedia contributors" status: active scope: public tags: ["biochemistry-methods", "lipids", "biotechnology", "mass-spectrometry"] description: "Study of complete lipid profile in organisms" topic_path: "science/biology" source: "https://en.wikipedia.org/wiki/Lipidomics" license: "CC BY-SA 4.0" wikipedia_page_id: 0 wikipedia_revision_id: 0

::summary Study of complete lipid profile in organisms ::

::figure[src="https://upload.wikimedia.org/wikipedia/commons/9/9d/Lipid_examples.png" caption="Examples of various lipid species."] ::

Lipidomics is the large-scale study of pathways and networks of cellular lipids in biological systems.{{cite journal |author=Wenk MR |title=The emerging field of lipidomics |journal=Nat Rev Drug Discov |volume=4 |issue=7 |pages=594–610 |date=July 2005 |pmid=16052242 |doi=10.1038/nrd1776 |s2cid=83931214 |author=Watson AD |title=Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems |journal=J. Lipid Res. |volume=47 |issue=10 |pages=2101–11 |date=October 2006 |pmid=16902246 |doi=10.1194/jlr.R600022-JLR200 |doi-access=free |author=Han X |title=Neurolipidomics: challenges and developments |journal=Front. Biosci. |volume=12 |issue= |pages=2601–15 |year=2007 |pmid=17127266 |pmc=2141543 |doi=10.2741/2258 |url=

Lipidomics research involves the identification and quantification of the thousands of cellular lipid molecular species and their interactions with other lipids, proteins, and other metabolites. Investigators in lipidomics examine the structures, functions, interactions, and dynamics of cellular lipids and the changes that occur during perturbation of the system.

Han and Gross{{cite journal |author=Han X, Gross RW |title=Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics |journal=J. Lipid Res. |volume=44 |issue=6 |pages=1071–9 |date=June 2003 |pmid=12671038 |doi=10.1194/jlr.R300004-JLR200 |last2=Gross |doi-access=free

In lipidomic research, a vast amount of information quantitatively describing the spatial and temporal alterations in the content and composition of different lipid molecular species is accrued after perturbation of a cell through changes in its physiological or pathological state. Information obtained from these studies facilitates mechanistic insights into changes in cellular function. Therefore, lipidomic studies play an essential role in defining the biochemical mechanisms of lipid-related disease processes through identifying alterations in cellular lipid metabolism, trafficking and homeostasis. The growing attention on lipid research is also seen from the initiatives underway of the LIPID Metabolites And Pathways Strategy (LIPID MAPS Consortium). and The European Lipidomics Initiative (ELIfe).

Structural diversity of lipids

Lipids are a diverse and ubiquitous group of compounds which have many key biological functions, such as acting as structural components of cell membranes, serving as energy storage sources and participating in signaling pathways. Lipids may be broadly defined as hydrophobic or amphipathic small molecules that originate entirely or in part from two distinct types of biochemical subunits or "building blocks": ketoacyl and isoprene groups. The huge structural diversity found in lipids arises from the biosynthesis of various combinations of these building blocks. For example, glycerophospholipids are composed of a glycerol backbone linked to one of approximately 10 possible headgroups and also to 2 fatty acyl/alkyl chains, which in turn may have 30 or more different molecular structures. In practice, not all possible permutations are detected experimentally, due to chain preferences depending on the cell type and also to detection limits - nevertheless several hundred distinct glycerophospholipid molecular species have been detected in mammalian cells.

Plant chloroplast thylakoid membranes however, have unique lipid composition as they are deficient in phospholipids. Also, their largest constituent, monogalactosyl diglyceride or MGDG, does not form aqueous bilayers. Nevertheless, dynamic studies reveal a normal lipid bilayer organisation in thylakoid membranes.

Experimental techniques

Lipid extraction

Most methods of lipid extraction and isolation from biological samples exploit the high solubility of hydrocarbon chains in organic solvents. Given the diversity in lipid classes, it is not possible to accommodate all classes with a common extraction method. The traditional Bligh/Dyer procedure {{cite journal |author=Bligh EG, Dyer WJ |title=A rapid method of total lipid extraction and purification |journal=Can J Biochem Physiol |volume=37 |issue=8 |pages=911–7 |date=August 1959 |pmid=13671378 |doi=10.1139/o59-099 |last2=Dyer |s2cid=7311923 uses chloroform/methanol-based protocols that include phase partitioning into the organic layer. However, several protocols now exist, with newer methods overcoming the shortcomings of older ones and solving problems associated with, for example, targeted lipid isolation or high throughput data collection {{cite journal |author=Furse S, Egmond MR, Killian, JA |title=Isolation of lipids from biological samples |journal=Mol Membr Biol |volume=32 |issue=3 |pages=55–64 |date=2015 |pmid=26212444 |doi=10.3109/09687688.2015.1050468 |url=https://www.tandfonline.com/doi/pdf/10.3109/09687688.2015.1050468 |last2=Egmond |last3=Killian |hdl=1874/329957 |s2cid=24537585 |hdl-access=free |url-access=subscription . Most protocols work relatively well for a variety of physiologically relevant lipids but they have to be adapted for species with particular properties and low-abundance and labile lipid metabolites{{cite book |author=Krank J, Murphy RC, Barkley RM, Duchoslav E, McAnoy A |volume=432 |pages=1–20 |year=2007 |pmid=17954211 |doi=10.1016/S0076-6879(07)32001-6 |series=Methods in Enzymology |isbn=978-0-12-373895-0 |last2=Murphy |last3=Barkley |last4=Duchoslav |last5=McAnoy |title=Lipidomics and Bioactive Lipids: Mass-Spectrometry–Based Lipid Analysis |chapter=Qualitative Analysis and Quantitative Assessment of Changes in Neutral Glycerol Lipid Molecular Species within Cells |author=Ivanova PT, Milne SB, Byrne MO, Xiang Y, Brown HA |volume=432 |pages=21–57 |year=2007 |pmid=17954212 |doi=10.1016/S0076-6879(07)32002-8 |series=Methods in Enzymology |isbn=978-0-12-373895-0 |last2=Milne |last3=Byrne |last4=Xiang |last5=Brown |title=Lipidomics and Bioactive Lipids: Mass-Spectrometry–Based Lipid Analysis |chapter=Glycerophospholipid Identification and Quantitation by Electrospray Ionization Mass Spectrometry |author=Deems R, Buczynski MW, Bowers-Gentry R, Harkewicz R, Dennis EA |volume=432 |pages=59–82 |year=2007 |pmid=17954213 |doi=10.1016/S0076-6879(07)32003-X |series=Methods in Enzymology |isbn=978-0-12-373895-0 |last2=Buczynski |last3=Bowers-Gentry |last4=Harkewicz |last5=Dennis |title=Lipidomics and Bioactive Lipids: Mass-Spectrometry–Based Lipid Analysis |chapter=Detection and Quantitation of Eicosanoids via High Performance Liquid Chromatography-Electrospray Ionization-Mass Spectrometry |s2cid=37207815 |url=https://escholarship.org/uc/item/9xs5q77r |author=McDonald JG, Thompson BM, McCrum EC, Russell DW |volume=432 |pages=145–70 |year=2007 |pmid=17954216 |doi=10.1016/S0076-6879(07)32006-5 |series=Methods in Enzymology |isbn=978-0-12-373895-0 |last2=Thompson |last3=McCrum |last4=Russell |title=Lipidomics and Bioactive Lipids: Mass-Spectrometry–Based Lipid Analysis |chapter=Extraction and Analysis of Sterols in Biological Matrices by High Performance Liquid Chromatography Electrospray Ionization Mass Spectrometry |author=Garrett TA, Guan Z, Raetz CR |volume=432 |pages=117–43 |year=2007 |pmid=17954215 |doi=10.1016/S0076-6879(07)32005-3 |series=Methods in Enzymology |isbn=978-0-12-373895-0 |last2=Guan |last3=Raetz |title=Lipidomics and Bioactive Lipids: Mass-Spectrometry–Based Lipid Analysis |chapter=Analysis of Ubiquinones, Dolichols, and Dolichol Diphosphate-Oligosaccharides by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry |author=Sullards MC, Allegood JC, Kelly S, Wang E, Haynes CA, Park H, Chen Y, Merrill AH |volume=432 |pages=83–115 |year=2007 |pmid=17954214 |doi=10.1016/S0076-6879(07)32004-1 |series=Methods in Enzymology |isbn=978-0-12-373895-0 |last2=Allegood |last3=Kelly |last4=Wang |last5=Haynes |last6=Park |last7=Chen |last8=Merrill Jr |title=Lipidomics and Bioactive Lipids: Mass-Spectrometry–Based Lipid Analysis |chapter=Structure-Specific, Quantitative Methods for Analysis of Sphingolipids by Liquid Chromatography–Tandem Mass Spectrometry: "Inside-Out" Sphingolipidomics .

Lipid separation

The simplest method of lipid separation is the use of thin layer chromatography (TLC). Although not as sensitive as other methods of lipid detection, it offers a rapid and comprehensive screening tool prior to more sensitive and sophisticated techniques. Solid-phase extraction (SPE) chromatography is useful for rapid, preparative separation of crude lipid mixtures into different lipid classes. This involves the use of prepacked columns containing silica or other stationary phases to separate glycerophospholipids, fatty acids, cholesteryl esters, glycerolipids, and sterols from crude lipid mixtures.{{cite journal |author=Kaluzny MA, Duncan LA, Merritt MV, Epps DE |title=Rapid separation of lipid classes in high yield and purity using bonded phase columns |journal=J. Lipid Res. |volume=26 |issue=1 |pages=135–40 |date=January 1985 |pmid=3973509 |doi=10.1016/S0022-2275(20)34412-6 |last2=Duncan |last3=Merritt |last4=Epps |doi-access=free High-performance liquid chromatography (HPLC or LC) is extensively used in lipidomic analysis to separate lipids prior to mass analysis. Separation can be achieved by either normal-phase (NP) HPLC or reverse-phase (RP) HPLC. For example, NP-HPLC effectively separates glycerophospholipids on the basis of headgroup polarity,{{cite journal |author=Malavolta M, Bocci F, Boselli E, Frega NG |title=Normal phase liquid chromatography-electrospray ionization tandem mass spectrometry analysis of phospholipid molecular species in blood mononuclear cells: application to cystic fibrosis |journal=J. Chromatogr. B |volume=810 |issue=2 |pages=173–86 |date=October 2004 |pmid=15380713 |doi=10.1016/j.jchromb.2004.07.001 |last2=Bocci |last3=Boselli |last4=Frega effectively separates fatty acids such as eicosanoids on the basis of chain length, degree of unsaturation and substitution.{{cite journal |author=Nakamura T, Bratton DL, Murphy RC |title=Analysis of epoxyeicosatrienoic and monohydroxyeicosatetraenoic acids esterified to phospholipids in human red blood cells by electrospray tandem mass spectrometry |journal=J Mass Spectrom |volume=32 |issue=8 |pages=888–96 |date=August 1997 |pmid=9269087 |doi=10.1002/(SICI)1096-9888(199708)32:83.0.CO;2-W |last2=Bratton |last3=Murphy |bibcode=1997JMSp...32..888N

Lipid detection

The progress of modern lipidomics has been greatly accelerated by the development of spectrometric methods in general and soft ionization techniques for mass spectrometry such as electrospray ionization (ESI), desorption electrospray ionization (DESI), and matrix-assisted laser desorption/ionization (MALDI){{cite book |author=Fuchs B, Schiller J |journal=Subcell. Biochem. |volume=49 |issue= |pages=541–65 |year=2008 |pmid=18751926 |doi=10.1007/978-1-4020-8831-5_21 |url= |series=Subcellular Biochemistry |isbn=978-1-4020-8830-8 |last2=Schiller |title=Lipids in Health and Disease |chapter=MALDI-TOF MS Analysis of Lipids from Cells, Tissues and Body Fluids does not cause extensive fragmentation, so that comprehensive detection of an entire range of lipids within a complex mixture can be correlated to experimental conditions or disease state. In addition, the technique of atmospheric pressure chemical ionization (APCI) has become increasingly popular for the analysis of nonpolar lipids.{{cite journal |author=Byrdwell WC |title=Atmospheric pressure chemical ionization mass spectrometry for analysis of lipids |journal=Lipids |volume=36 |issue=4 |pages=327–46 |date=April 2001 |pmid=11383683 |doi=10.1007/s11745-001-0725-5 |s2cid=4017177 |url=

::figure[src="https://upload.wikimedia.org/wikipedia/commons/1/1a/Tandem_ms.png" caption="Schema showing detection of a fatty acid by LC-MS/MS using a linear ion-trap instrument and an electrospray (ESI) ion source."] ::

[[Electrospray ionization|ESI MS]]

ESI-MS was initially developed by Fenn and colleagues for analysis of biomolecules.{{cite journal |author=Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM |title=Electrospray ionization for mass spectrometry of large biomolecules |journal=Science |volume=246 |issue=4926 |pages=64–71 |date=October 1989 |pmid=2675315 |doi=10.1126/science.2675315 |bibcode=1989Sci...246...64F |last2=Mann |last3=Meng |last4=Wong |last5=Whitehouse |citeseerx=10.1.1.522.9458 |author=Murphy RC, Fiedler J, Hevko J |title=Analysis of nonvolatile lipids by mass spectrometry |journal=Chem. Rev. |volume=101 |issue=2 |pages=479–526 |date=February 2001 |pmid=11712255 |doi=10.1021/cr9900883 |last2=Fiedler |last3=Hevko |author=Gross RW, Han X |volume=433 |pages=73–90 |year=2007 |pmid=17954229 |doi=10.1016/S0076-6879(07)33004-8 |series=Methods in Enzymology |isbn=978-0-12-373966-7 |last2=Han |title=Lipidomics and Bioactive Lipids: Specialized Analytical Methods and Lipids in Disease |chapter=Lipidomics in Diabetes and the Metabolic Syndrome

[[Desorption electrospray ionization|DESI MS]]

DESI mass spectrometry is an ambient ionization technique developed by Professor Zoltan Takáts, et al., in Professor Graham Cooks' group from Purdue University. It combines the ESI and desorption ionization techniques, by directing an electrically charged mist to the sample surface that is a few millimeters away. The technique has been successfully applied to lipidomics as imaging tool to map the lipid distributions within tissue specimens. One of the advantages of DESI MS is that no matrix is required for tissue preparation, allowing multiple consecutive measurements on the same tissue specimen. DESI MS can also be used for imaging of lipids from tissue sections.

[[Matrix-assisted laser desorption/ionization|MALDI MS]]

MALDI mass spectrometry is a laser-based soft-ionization method often used for analysis of large proteins, but has been used successfully for lipids. The lipid is mixed with a matrix, such as 2,5-dihydroxybenzoic acid, and applied to a sample holder as a small spot. A laser is fired at the spot, and the matrix absorbs the energy, which is then transferred to the analyte, resulting in ionization of the molecule. MALDI-Time-of-flight (MALDI-TOF) MS has become a very promising approach for lipidomics studies, particularly for the imaging of lipids from tissue slides.{{cite journal |author=Schiller J, Suss R, Fuchs B, Muller M, Zschornig O, Arnold K |title=MALDI-TOF MS in lipidomics |journal=Front. Biosci. |volume=12 |issue= |pages=2568–79 |year=2007 |pmid=17127263 |doi=10.2741/2255 |url= |last2=Suss |last3=Fuchs |last4=Muller |last5=Zschornig |last6=Arnold |doi-access=free

APCI MS

The source for APCI is similar to ESI except that ions are formed by the interaction of the heated analyte solvent with a corona discharge needle set at a high electrical potential. Primary ions are formed immediately surrounding the needle, and these interact with the solvent to form secondary ions that ultimately ionize the sample. APCI is particularly useful for the analysis of nonpolar lipids such as triacylglycerols, sterols, and fatty acid esters.{{cite journal |author=Byrdwell WC |title=Dual parallel liquid chromatography with dual mass spectrometry (LC2/MS2) for a total lipid analysis |journal=Front. Biosci. |volume=13 |issue=13 |pages=100–20 |year=2008 |pmid=17981531 |doi=10.2741/2663 |url=http://www.bioscience.org/2008/v13/af/2663/fulltext.htm |doi-access=free

Imaging techniques

The high sensitivity of DESI in the lipid range makes it a powerful technique for the detection and mapping of lipids abundances within tissue specimens. Recent developments in MALDI methods have enabled direct detection of lipids in-situ. Abundant lipid-related ions are produced from the direct analysis of thin tissue slices when sequential spectra are acquired across a tissue surface that has been coated with a MALDI matrix. Collisional activation of the molecular ions can be used to determine the lipid family and often structurally define the molecular species. These techniques enable detection of phospholipids, sphingolipids and glycerolipids in tissues such as heart, kidney and brain. Furthermore, distribution of many different lipid molecular species often define anatomical regions within these tissues.{{cite journal |author=Murphy RC, Hankin JA, Barkley RM |title=Imaging of lipid species by MALDI mass spectrometry |journal=J. Lipid Res. |volume=50 Suppl |issue=Supplement |pages=S317–22 |date=December 2008 |pmid=19050313 |doi=10.1194/jlr.R800051-JLR200 |doi-access=free |pmc=2674737 |last2=Hankin |last3=Barkley

Lipid profiling

::figure[src="https://upload.wikimedia.org/wikipedia/commons/f/f2/Flexibility_of_a_eukaryotic_lipidome_-_insights_from_yeast_lipidomics-Klose,_Surma_2012_fig2.svg" caption="bibcode=2012PLoSO...735063K}}"] ::

Lipid profiling is a targeted metabolomics platform that provides a comprehensive analysis of lipid species within a cell or tissue. Profiling based on electrospray ionization tandem mass spectrometry (ESI-MS/MS) is capable of providing quantitative data and is adaptable to high throughput analyses. The powerful approach of transgenics, namely deletion and/or overexpression of a gene product coupled with lipidomics, can give valuable insights into the role of biochemical pathways.{{cite journal |author=Serhan CN, Jain A, Marleau S, Clish C, Kantarci A, Behbehani B, Colgan SP, Stahl GL, Merched A, Petasis NA, Chan L, Van Dyke TE |title=Reduced inflammation and tissue damage in transgenic rabbits overexpressing 15-lipoxygenase and endogenous anti-inflammatory lipid mediators |journal=J. Immunol. |volume=171 |issue=12 |pages=6856–65 |date=December 2003 |pmid=14662892 |doi=10.4049/jimmunol.171.12.6856 |last2=Jain |last3=Marleau |last4=Clish |last5=Kantarci |last6=Behbehani |last7=Colgan |last8=Stahl |last9=Merched |last10=Petasis |last11=Chan |last12=Van Dyke |doi-access=free |author=Devaiah SP, Roth MR, Baughman E, Li M, Tamura P, Jeannotte R, Welti R, Wang X |title=Quantitative profiling of polar glycerolipid species from organs of wild-type Arabidopsis and a phospholipase Dalpha1 knockout mutant |journal=Phytochemistry |volume=67 |issue=17 |pages=1907–24 |date=September 2006 |pmid=16843506 |doi=10.1016/j.phytochem.2006.06.005 |last2=Roth |last3=Baughman |last4=Li |last5=Tamura |last6=Jeannotte |last7=Welti |last8=Wang |bibcode=2006PChem..67.1907D |author=Ejsing CS, Moehring T, Bahr U, Duchoslav E, Karas M, Simons K, Shevchenko A |title=Collision-induced dissociation pathways of yeast sphingolipids and their molecular profiling in total lipid extracts: a study by quadrupole TOF and linear ion trap-orbitrap mass spectrometry |journal=J Mass Spectrom |volume=41 |issue=3 |pages=372–89 |date=March 2006 |pmid=16498600 |doi=10.1002/jms.997 |last2=Moehring |last3=Bahr |last4=Duchoslav |last5=Karas |last6=Simons |last7=Shevchenko |bibcode=2006JMSp...41..372E

Informatics

A major challenge for lipidomics, in particular for MS-based approaches, lies in the computational and bioinformatic demands of handling the large amount of data that arise at various stages along the chain of information acquisition and processing.{{cite journal |author1=Subramaniam S |author2=Fahy E |author3=Gupta S |author4=Sud M |author5=Byrnes RW |author6=Cotter D |author7=Dinasarapu AR |author8=Maurya MR |title=Bioinformatics and Systems Biology of the Lipidome |journal=Chemical Reviews |volume=111 |issue=10 |pages=6452–6490 |year=2011 |doi=10.1021/cr200295k |pmid=21939287 |pmc=3383319 |author=Yetukuri L, Katajamaa M, Medina-Gomez G, Seppänen-Laakso T, Vidal-Puig A, Oresic M |title=Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis |journal=BMC Syst Biol |volume=1 |page=12 |year=2007 |pmid=17408502 |pmc=1839890 |doi=10.1186/1752-0509-1-12 |last2=Katajamaa |last3=Medina-Gomez |last4=Seppänen-Laakso |last5=Vidal-Puig |last6=Oresic |doi-access=free |author=Katajamaa M, Miettinen J, Oresic M |title=MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data |journal=Bioinformatics |volume=22 |issue=5 |pages=634–6 |date=March 2006 |pmid=16403790 |doi=10.1093/bioinformatics/btk039 |last2=Miettinen |last3=Oresic |doi-access=free |author=Lutz U, Lutz RW, Lutz WK |title=Metabolic profiling of glucuronides in human urine by LC-MS/MS and partial least-squares discriminant analysis for classification and prediction of gender |journal=Anal. Chem. |volume=78 |issue=13 |pages=4564–71 |date=July 2006 |pmid=16808466 |doi=10.1021/ac0522299 |last2=Lutz |last3=Lutz |author=Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M |title=KEGG Atlas mapping for global analysis of metabolic pathways |journal=Nucleic Acids Res. |volume=36 |issue=Web Server issue |pages=W423–6 |date=July 2008 |pmid=18477636 |pmc=2447737 |doi=10.1093/nar/gkn282 |url=|last2=Yamada |last3=Hamajima |last4=Itoh |last5=Katayama |last6=Bork |last7=Goto |last8=Kanehisa |author=Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, Merrill AH, Murphy RC, Raetz CR, Russell DW, Subramaniam S |title=LMSD: LIPID MAPS structure database |journal=Nucleic Acids Res. |volume=35 |issue=Database issue |pages=D527–32 |date=January 2007 |pmid=17098933 |pmc=1669719 |doi=10.1093/nar/gkl838 |url=|last2=Fahy |last3=Cotter |last4=Brown |last5=Dennis |last6=Glass |last7=Merrill Jr |last8=Murphy |last9=Raetz |last10=Russell |last11=Subramaniam |author=Cotter D, Maer A, Guda C, Saunders B, Subramaniam S |title=LMPD: LIPID MAPS proteome database |journal=Nucleic Acids Res. |volume=34 |issue=Database issue |pages=D507–10 |date=January 2006 |pmid=16381922 |pmc=1347484 |doi=10.1093/nar/gkj122 |url=|last2=Maer |last3=Guda |last4=Saunders |last5=Subramaniam |author=Yetukuri L, Ekroos K, Vidal-Puig A, Oresic M |title=Informatics and computational strategies for the study of lipids |journal=Mol Biosyst |volume=4 |issue=2 |pages=121–7 |date=February 2008 |pmid=18213405 |doi=10.1039/b715468b |last2=Ekroos |last3=Vidal-Puig |last4=Oresic

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biochemistry-methodslipidsbiotechnologymass-spectrometry