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LIPID MAPS Classification updates
(as of August 20th, 2008)Fahy, E., Subramaniam, S., Brown, H. A., Glass, C. K., Merrill, A. H., Jr., Murphy, R. C., Raetz, C. R., Russell, D. W., Seyama, Y., Shaw, W., Shimizu, T., Spener, F., van Meer, G., VanNieuwenhze, M. S., White, S. H., Witztum, J. L., and Dennis, E. A. (2005) A comprehensive classification system for lipids, J. Lipid Res., 46, 839-861. PubMed ID: 15722563.
Since then, a substantial number of updates and improvements have been made to the classification system, and these are described below:
Overview of classification updates
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Additional classes and subclasses
In response to worldwide interest in the lipid classification system, the scope has been expanded to cover lipids from non-mammalian sources such as plants, bacteria, fungi, algae and marine organisms. In order to accomplish this, several new lipid classes have been added, such as fatty acyl glycosides, glycosyldiradylglycerols, various sterol skeletons. The polyketide category has also been revised comprehensively. Details of the changes are listed by category below. -
Removal of classes based on lipid source
In keeping with the theme of having a classification scheme dictated by molecular structure and function, the sterol lipid subclasses Phytosterols, Marine sterols and Fungal sterols were retired because these refer to the lipid source (marine) or biological kingdom (plants,fungi). It is possible to identify a particular sterol in more than one of these 3 sources. These subclasses have been replaced by a new set of subclasses based on the carbon skeleton of the sterol core structure (Ergosterols, Gorgosterols, Furostanols,etc.). The details are outlined under the Sterol lipids section below. -
Adoption of existing natural products classification hierarchies for isoprenoids and polyketides
Whereas the focus of the LIPID MAPS consortium is mainly concerned with mammalian lipids, the natural products chemistry and medicinal chemistry literature describes tens of thousands of molecules which fall under the scope of lipids, based on their biosynthetic origin. In particular isoprenoids and polyketides from diverse sources such as plant, fungi, algae, bacteria and marine invertebrates and are well documented and have been reviewed and classified in detail. In particular, the Dictionary of Natural Products, a database available from Chapman & Hall/CRC (see website) has a classification hierarchy shown in this pdf document which covers polyketides and isoprenoids in depth. The LIPID MAPS classification system has now incorporated some of these hierarchies relevant to natural products, with a view to covering both mammalian and non-mammalian lipids comprehensively.
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Expansion of classification levels
It was recognized that additional levels of granularity were required to classify certain types of lipids and that the current 3-level system of category/main class/sub class needed to be expanded. For example, in the Prenol lipids category the sesquiterpene(C 15) subclass contains approximately 90 known variants based on their carbon skeletons (Bisabolanes, Germacranes, etc.). A 4th level of detail has been added to the LIPID MAPS classifcation system in order to handle cases such as these.
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Expansion of LM_ID identifier
As a consequence of adding an extra level of classification detail, the length of the LM_ID identifier was lengthened from 12 characters to 14 in cases where a lipid defined with 4 levels of classification is being described. In this case, characters #9 and 10 specify the level-4 class . It should be emphasized that all lipids which do not require a 4th level of detail (i.e. the vast majority of them) still use a 12-digit LM_ID identifier.Characters Description Example Comments 1-2 Fixed "LM" designation LM Always LM 3-4 2-letter category code FA One of 8 categories 5-6 2-digit class code 03 - 7-8 2-digit subclass code 02 May be '00' (no subclass) 9-10 2-digit class level-4 code 02 Only used for lipids with 4 class levels Last 4 digits Unique 4-character identifier within subclass 7312 - -
Changes to Glycerophospholipid abbreviations
In response to several requests from knowledgeable lipid experts, the Glycerophospholipid abbreviation system has been changed to the more universally used PC/PE/PS/PA/PI system (replacing GPCho/GPEtn/GPSer/GPA/GPI). All glycerophospholipids in the LIPID MAPS structure database and LIPID MAPS standards database, as well as all the glycerophospholipids drawing tools and MS prediction tools have been updated to conform to this new abbreviation format. The details of the changes are shown in a table under the Glycerophospholipid lipids section below. -
Use of expandable/collapsible menus on website
This is simply a cosmetic change in which there is an option to view the classification system of each lipid category as a top-level outline of main classes, and then click on the '+' icon of a main class of interest to view the corresponding sub class. This feature is convenient in the case of categories such as Glycerophospholipids and Prenol lipids which have large numbers of subclasses and/or 4th level classes.
See the classification page to view this feature.
Details of classification updates by lipid category
Fatty acyls [FA] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Hydroxyeicosatrienoic acids [FA0305] Hydroxyeicosatetraenoic acids [FA0306] Hydroxyeicosapentaenoic acids [FA0307]
changed to:
Added:
N-acyl amides [FA0802]
Added:
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Glycerolipids [GL] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Removed: Alkylacylglycerols [GL0202]
Added:
Removed:
Added:
Positional isomers specifications in LIPID MAPS abbreviations for glycerolipids Instead of drawing all possible structural isomers explicitly for Diradylglycerols and Triradylglycerols, the LIPID MAPS abbreviation scheme supports the isomeric specification. A suffix containing 'iso' along with the number of possible isomers is appended to the abbreviation (e.g. [iso2],[iso6]) and a single unique LM_ID is assigned. The structure assigned to the LM_ID corresponds to the radyl substitution shown in the abbreviation. An option is provided to display the other isomers in the group. The [rac] designation refers to racemic mixtures due to substitution at the sn1 and sn3 positions of glycerol.
Examples:
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Glycerophospholipids [GP] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Added: 1-acyl,2-alkylglycerophosphocholines [GP0108]
1-alkyl glycerophosphocholines [GP0106]
Added:
1-alkyl glycerophosphoethanolamines [GP0206]
1-alkyl glycerophosphoethanoserines [GP0306]
1-alkyl glycerophosphoglycerols [GP0406]
1-alkyl glycerophosphoethanophosphates [GP0506]
1-alkyl glycerophosphoethanoinositols [GP0606]
1-alkyl glycerophosphoethanoinositol monophosphates [GP0706]
1-alkyl glycerophosphoethanoinositol bisphosphates [GP0805]
1-alkyl glycerophosphoethanoinositol trisphosphates [GP0905]
1-alkyl glycerophosphates [GP1006]
1-alkyl glycerophosphoethanophosphates [GP0506]
Added:
1-alkyl glycerophosphoglycerophosphodiradylglycerols [GP1208]
CDP-1-alkyl glycerols [GP0506]
Removed:
Added:
1-alkyl glycerophosphoinositolglycans [GP1505]
1-alkyl glycerophosphonocholines [GP1606]
1-alkyl glycerophosphonoethanolamines [GP1706] Changes in LIPID MAPS abbreviations for glycerophospholipids
Stereochemistry specifications in LIPID MAPS abbreviations for glycerophospholipids For molecules with opposite (S) stereochemistry at C2 of the glycerol group and attachment of the headgroup at the sn1 position, the stereochemistry specification of [S] is appended to the abbreviation. The 'Headgroup(sn3/sn2)' abbreviation format is used. For molecules with unknown stereochemistry at the C2 carbon of the glycerol group, the stereochemistry specification of [U] is appended to the abbreviation and the structure is drawn with C2 stereochemistry unspecified. For example: Abbreviation - PC(16:0/18:1(9E)[U]); LMID - LMGP01010582; Systematic name - 1-hexadecanoyl-2-(9E-octadecenoyl)-sn-glycero-3-phosphocholine.
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Sphingolipids [SP] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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No changes
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Sterol lipids [ST] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Removed: Phytosterols and derivatives [ST0103] Marine sterols and derivatives [ST0104] Fungal sterols and derivatives [ST0105]
Added:
Added:
Added:
Removed:
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Prenol Lipids [PR] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Added: Extra level of subclassification to C10 isoprenoids (monoterpenes) [PR0102] Acyclic monoterpenoids [PR010201] etc., etc.
Extra level of subclassification to C15 isoprenoids (sesquiterpenes) [PR0103]
Extra level of subclassification to C20 isoprenoids (diterpenes) [PR0104]
Extra level of subclassification to C25 isoprenoids (sesterterpenes) [PR0105]
Extra level of subclassification to C30 isoprenoids (triterpenes) [PR0106]
Added:
Added:
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Saccharolipids [SL] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Added: Other acyl sugars [SL05]
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Polyketides [PR] | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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(This category was completely revised)
Removed:
Added:
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