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Description | Lipidomics |
Contact | |
Primary citation | PMID 17584797 |
Release date | 2003 |
Access | |
Website | www.lipidmaps.org |
LIPID MAPS (Lipid Metabolites and Pathways Strategy) is a web portal designed to be a gateway to Lipidomics resources. The resource has spearheaded a classification of biological lipids, dividing them into eight general categories. [1] LIPID MAPS provides standardised methodologies for mass spectrometry analysis of lipids, e.g. [2] [3] [4]
LIPID MAPS has been cited as evidence of a growing appreciation of the study of lipid metabolism [5] and the rapid development and standardisation of the lipidomics field [6] [7]
Key LIPID MAPS resources include:
Tools available from LIPID MAPS enable scientists to identify likely lipids in their samples from mass spectrometry data, a common method to analyse lipids in biological specimens. In particular, LipidFinder [10] enables analysis of MS data. Tutorials and educational material on lipids are also available at the site. [11]
LIPID MAPS was founded in 2003 with NIH funding. [13] Since 2016, it has been a joint project between the University of Cardiff led by Prof Valerie O'Donnell, the Babraham Institute under Michael Wakelam, and UCSD scientists Shankar Subramaniam and Ed Dennis funded by the Wellcome Trust. Wakelam's obituary describes LIPID MAPS as unifying the field of lipidomics. [14]
LIPID MAPS is sponsored by Avanti Polar lipids and Cayman Chemicals
Lipids are a broad group of organic compounds which include fats, waxes, sterols, fat-soluble vitamins, monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing energy, signaling, and acting as structural components of cell membranes. Lipids have applications in the cosmetic and food industries, and in nanotechnology.
Lipidomics is the large-scale study of pathways and networks of cellular lipids in biological systems The word "lipidome" is used to describe the complete lipid profile within a cell, tissue, organism, or ecosystem and is a subset of the "metabolome" which also includes other major classes of biological molecules. Lipidomics is a relatively recent research field that has been driven by rapid advances in technologies such as mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, fluorescence spectroscopy, dual polarisation interferometry and computational methods, coupled with the recognition of the role of lipids in many metabolic diseases such as obesity, atherosclerosis, stroke, hypertension and diabetes. This rapidly expanding field complements the huge progress made in genomics and proteomics, all of which constitute the family of systems biology.
Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the complete set of metabolites in a biological cell, tissue, organ, or organism, which are the end products of cellular processes. Messenger RNA (mRNA), gene expression data, and proteomic analyses reveal the set of gene products being produced in the cell, data that represents one aspect of cellular function. Conversely, metabolic profiling can give an instantaneous snapshot of the physiology of that cell, and thus, metabolomics provides a direct "functional readout of the physiological state" of an organism. There are indeed quantifiable correlations between the metabolome and the other cellular ensembles, which can be used to predict metabolite abundances in biological samples from, for example mRNA abundances. One of the ultimate challenges of systems biology is to integrate metabolomics with all other -omics information to provide a better understanding of cellular biology.
The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism as well as exogenous chemicals that are not naturally produced by an organism.
BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is an electronic resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction. Kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a web-based user interface that allows a convenient and sophisticated access to the data.
Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.
A simple lipid is a fatty acid ester of different alcohols and carries no other substance. These lipids belong to a heterogeneous class of predominantly nonpolar compounds, mostly insoluble in water, but soluble in nonpolar organic solvents such as chloroform and benzene.
The lipidome refers to the totality of lipids in cells. Lipids are one of the four major molecular components of biological organisms, along with proteins, sugars and nucleic acids. Lipidome is a term coined in the context of omics in modern biology, within the field of lipidomics. It can be studied using mass spectrometry and bioinformatics as well as traditional lab-based methods. The lipidome of a cell can be subdivided into the membrane-lipidome and mediator-lipidome.
U2 small nuclear ribonucleoprotein A' is a protein that in humans is encoded by the SNRPA1 gene.
60S ribosomal protein L28 is a protein that in humans is encoded by the RPL28 gene.
60S ribosomal protein L36 is a protein that in humans is encoded by the RPL36 gene.
40S ribosomal protein S24 is a protein that in humans is encoded by the RPS24 gene.
60S ribosomal protein L35 is a protein that in humans is encoded by the RPL35 gene.
Pleiotropic regulator 1 is a protein that in humans is encoded by the PLRG1 gene.
BIOBASE is an international bioinformatics company headquartered in Wolfenbüttel, Germany. The company focuses on the generation, maintenance, and licensing of databases in the field of molecular biology, and their related software platforms.
Rolf Apweiler is a director of European Bioinformatics Institute (EBI) part of the European Molecular Biology Laboratory (EMBL) with Ewan Birney.
The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in the human body. It has been created by the Human Metabolome Project funded by Genome Canada and is one of the first dedicated metabolomics databases. The HMDB facilitates human metabolomics research, including the identification and characterization of human metabolites using NMR spectroscopy, GC-MS spectrometry and LC/MS spectrometry. To aid in this discovery process, the HMDB contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data (Fig. 1–3). The chemical data includes 41,514 metabolite structures with detailed descriptions along with nearly 10,000 NMR, GC-MS and LC/MS spectra.
Ronald Charles Beavis is a Canadian protein biochemist, who has been involved in the application of mass spectrometry to protein primary structure, with applications in the fields of proteomics and analytical biochemistry. He has developed methods for measuring the identity and post-translational modification state of proteins obtained from biological samples using mass spectrometry. He is currently best known for developing new methods for analyzing proteomics data and applying the results of these methods to problems in computational biology.
BacDive is a bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity.