Lipid MAPS

Finally, we will identify the structure of enriched ions by using accurate mass (obtained during our standard MS experiments) and searching metabolite databases, such as METLIN [75], PubChem [76], or the lipid MAPS [77] for... 

Table 11.1 Relationship of tocopherols and tochotrienols to other lipids. Eight categories of lipids according to the Lipid-MAPS classification (Fahy et al., 2005).

Category Abbrev Current number of lipids in this Lipid-MAPS category Examples... 

More recently, a third omics field, lipidomics, was developed. Lipidomics was developed to attempt to provide a system in which to quantitatively profile all of the lipid molecules in a given species or in a tissue within that species (Han, 2011 Welti, 2011). Not surprisingly, a new nomenclature system has been developed to help to define and catalog the various lipids in the lipidome of each species. In this system, tocopherols and tocotrienols are part of the category called prenols (Table 11.1). Currently, the main database for lipidomics information in the USA is the LIPID-MAPS (2011) and its Prenol category contains the four known tocopherols (oc, (3, y, 5), four known tocotrienols (a, [3, y, 5), and a total of 1177 Prenols. Each of the eight individual tocopherols and tocotrienols are sometimes referred to as vitamers. 

Common Name Abbrev Lipid-MAPS number" CAS Number Formula Mass... 

The mentioned data management systems are only first steps toward comprehensive lipid databases and global lipid networks. An example for such a data bank is LIPIDMAPS (http //www.lipidmaps.org), which covers structures and annotations of biologically relevant lipids (43). The structures originate from the core laboratories of the LIPIDMAPS consortium and their partners. In this database, users can search the LIPID MAPS proteome database using either text-based or structure-based search options. In addition to LIPIDMAPS, other databases in Europe (http //www.lipidomics.net) and Japan (http //www.lipidbank.jp) have been initiated. 

Sud M, Fahy E, Cotter D, Brown A, Dennis EA, Glass CK, et al. LMSD LIPID MAPS structure database. Nucleic Acids Res. 2007 35 D527-D532. 

LIPID MAPS http .//www.lipidmaps. org/ Lipidomics gateway... 

Sources for specific omics studies are also available. For instance, tools such as the RNA-Seq Atlas [17], Human Protein Atlas (HPA) [18], and the Human Metabolome Database (HMDB) [19] are useful for systemic genomic, proteomic, and metabolo-mics studies of human beings. LIPID Metabolites and Pathways Strategy (LIPID MAPS) [20] is a lipidomics gateway, an integrative platform for studies in lipid biology. More resources and updated links can be found at the Biomarkers portal (see Table 1). 

Fahy E, Sud M, Cotter D, Subramaniam S (2007) LIPID MAPS online tools for lipid research. Nucleic Acids Res 35 W606-W612... 

LIPID Metabolites and Pathway Strategy (LIPID MAPS)... 

Kyoto University/ Tokyo University LIPID MAPS Bioinformatics Core... 

Schmelzer, K., Fahy, E., Subramaniam, S. and Dennis, E.A., The lipid maps initiative in lipidomics. Methods Enzymol 432 (2007) 171-183. 

A comprehensive classification system for lipids with broad support in the lipid research community can be found at the Lipid Maps Structure Database (www. Upidmaps.org). The Lipid Maps Structure Database currently catalogs over 10,000 structures. 

The LIPID Metabolites and Pathways Strategy (LIPID MAPS) consortium is identifying, characterizing, and classifying the components of the lipidome and developing a... 

For MS analysis to be quantitative, investigators must have access to a sufficiently complete series of internal standards that can be added to samples so their recoveries can be used to account for differences in extraction efficiency, ionization, and fragmentation. This is still a major limitation to a complete, quantitative sphingolipidomic analysis however, a number of individual internal standards and internal standard cocktails have been identified by the Lipid Maps Consortium (http //www.lipidmaps.org) and are commercially available from Avanti Polar Lipids (Alabaster, AL). A related challenge is to... 

Fundamentally, lipidomics can be defined as the qualitative and quantitative determination of all lipid molecular species in a biological fluid, tissue, or cell type. This goal is impractical for individual groups of workers, but is a realistic aim, at least for the more abundant lipids, for consortia of lipid scientists. Such consorha exist and the Lipid Maps (http // www.lipidmaps.org/) grouping in the LFnited States has already published results from extensive joint studies of the human plasma lipidome... 

Figure 2.10 Reconstructed MRM traces for Bligh/Dyer extract of sterols from mouse brain. Known sterols are labeled, unknown compounds with a sterollike signature are indicated by . MS/MS of the respective steroids can be found at Lipid Maps http //www.lipidmaps.org/data/standards/standards. php lipidclass=LMST. (Reproduced with permission from McDonald, J. G. et al., 2007, Extraction and Analysis of Sterols in Biological Matrices by High-Performance Liquid Chromatography Electrospray Ionization Mass Spectrometry, Methods Enzymol. 432 145-70.)...

Murphy, R.C., LIPID MAPS Lipidomics Workshop. (2009) Future directions tissue and ceU imaging. Available at http //www.lipidmaps.org/resources/lipidmapspresenta-tions/EB2009/MurphyEB2(X)9.pdf. 

The most recent definition of lipids was provided by a group of lipid chemists who formed the consortium of lipid metabolites and pathways strategy (Lipid MAPS). They defined lipids based on the origin of the lipid structures as hydrophobic or amphipathic small molecules that may originate entirely or, in part, by carbanion-based condensations of thioesters (fatty acids, polyketides, etc.) and/or by carbocation-based condensations of isoprene units (prenols, sterols, etc.). In this book, this definition, its classification (see the following), and its recommended nomenclature are largely accepted. 

Figure 11 Examples of glycerophospholipid classes. Different structures of the moiety X, which are connected to the phosphate and exemplified in the box, determine the individual classes of GPL as indicated with abbreviations that are commonly used in the hterature and adapted by the Lipid MAPS consortium.

Analysis of individual lipid species of a class in the Lipid MAPS protocols was largely developed based on reversed-phase LC-MS. For example, in the protocol for eicosanoid analysis, a C18 column (250 X 2.1 mm) was employed and a specific gradient from mobile phase A (water-acetonitrile-formic acid, 63 37 0.02, v/v/v) to B (acetonitrile-isopropanol, 50 50, v/v) was applied [71]. Individual eicosanoid species were detected by using the MRM approach and quantified in comparison to the relevant internal standard. 

The Lipid MAPS Structure Database (LMSD) is a relational database containing structures and annotations of biologically relevant lipids. As of the mid-2015, LMSD contains over 40,360 unique lipid structures and is the largest public database in the world specifically for lipids. The structures of lipids in the database are from the following sources [6] ... 

Lipid MAPS consortium s core laboratories and partners. 

Usage of hierarchical classification and consistent nomenclature based on a comprehensive classification scheme proposed by Lipid MAPS. 

A unique Lipid MAPS ID number assigned to individual lipid structure, which reflects its position in the classification hierarchy. 

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