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• W3091953196 abstract "A comprehensive and standardized system to report lipid structures analyzed by MS is essential for the communication and storage of lipidomics data. Herein, an update on both the LIPID MAPS classification system and shorthand notation of lipid structures is presented for lipid categories Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). With its major changes, i.e., annotation of ring double bond equivalents and number of oxygens, the updated shorthand notation facilitates reporting of newly delineated oxygenated lipid species as well. For standardized reporting in lipidomics, the hierarchical architecture of shorthand notation reflects the diverse structural resolution powers provided by mass spectrometric assays. Moreover, shorthand notation is expanded beyond mammalian phyla to lipids from plant and yeast phyla. Finally, annotation of atoms is included for the use of stable isotope-labeled compounds in metabolic labeling experiments or as internal standards. This update on lipid classification, nomenclature, and shorthand annotation for lipid mass spectra is considered a standard for lipid data presentation. A comprehensive and standardized system to report lipid structures analyzed by MS is essential for the communication and storage of lipidomics data. Herein, an update on both the LIPID MAPS classification system and shorthand notation of lipid structures is presented for lipid categories Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). With its major changes, i.e., annotation of ring double bond equivalents and number of oxygens, the updated shorthand notation facilitates reporting of newly delineated oxygenated lipid species as well. For standardized reporting in lipidomics, the hierarchical architecture of shorthand notation reflects the diverse structural resolution powers provided by mass spectrometric assays. Moreover, shorthand notation is expanded beyond mammalian phyla to lipids from plant and yeast phyla. Finally, annotation of atoms is included for the use of stable isotope-labeled compounds in metabolic labeling experiments or as internal standards. This update on lipid classification, nomenclature, and shorthand annotation for lipid mass spectra is considered a standard for lipid data presentation. Lipids have become increasingly recognized as the central metabolites affecting human physiology and pathophysiology, and LIPID MAPS has recently expanded its tools, resources, data, and training as a free resource dedicated to serving the lipid research community (1O'Donnell V.B. Dennis E.A. Wakelam M.J.O. Subramaniam S. LIPID MAPS: serving the next generation of lipid researchers with tools, resources, data, and training.Sci. Signal. 2019; 12eaaw2964 Crossref PubMed Scopus (33) Google Scholar). Following development of the LIPID MAPS nomenclature, classification, and structural representation system (2Fahy E. Subramaniam S. Brown H.A. Glass C.K. Merrill Jr., A.H. Murphy R.C. Raetz C.R. Russell D.W. Seyama Y. Shaw W. et al.A comprehensive classification system for lipids.J. Lipid Res. 2005; 46: 839-861Abstract Full Text Full Text PDF PubMed Scopus (943) Google Scholar, 3Fahy E. Subramaniam S. Murphy R.C. Nishijima M. Raetz C.R. Shimizu T. Spener F. van Meer G. Wakelam M.J. Dennis E.A. Update of the LIPID MAPS comprehensive classification system for lipids.J. Lipid Res. 2009; 50: S9-S14Abstract Full Text Full Text PDF PubMed Scopus (852) Google Scholar), an initial shorthand nomenclature was proposed (4Liebisch G. Vizcaino J.A. Köfeler H. Trötzmüller M. Griffiths W.J. Schmitz G. Spener F. Wakelam M.J. Shorthand notation for lipid structures derived from mass spectrometry.J. Lipid Res. 2013; 54: 1523-1530Abstract Full Text Full Text PDF PubMed Scopus (463) Google Scholar), which included a structural hierarchy as shown by others as well (5Ekroos K. From molecular lipidomics to validated clinical diagnosis.in: Ekroos K. Lipidomics: Technologies and Applications. Wiley-VCH, Weinheim, Germany2012: 1-16Crossref Scopus (10) Google Scholar, 6Porta Siegel T. Ekroos K. Ellis S.R. Reshaping Lipid Biochemistry by Pushing Barriers in Structural Lipidomics.Angew. Chem. Int. Ed. Engl. 2019; 58: 6492-6501Crossref PubMed Scopus (30) Google Scholar). These were the first attempts to provide rules for reporting mass spectrometric data dependent on the power for structural resolution of lipids by the instrumental set-ups in use at that time. Today, we recognize that the field has evolved in often diverging ways and that this has not enabled a unifying naming convention to be adopted throughout. For example, alternative shorthand notation has evolved for some lipid classes, a plethora of newly determined structures for lipids from various classes and phylogenetic kingdoms (higher plants and yeasts) have been described, and progress in the technological development of mass spectrometers with greater structural resolution as well as advances in automation in interpreting high-throughput data has occurred. To address this, it is the aim of this report to take into account these developments and to present an update on the LIPID MAPS classification and a pragmatic highly usable shorthand notation for those active in lipid research. This update will focus on five of the eight LIPID MAPS categories (2Fahy E. Subramaniam S. Brown H.A. Glass C.K. Merrill Jr., A.H. Murphy R.C. Raetz C.R. Russell D.W. Seyama Y. Shaw W. et al.A comprehensive classification system for lipids.J. Lipid Res. 2005; 46: 839-861Abstract Full Text Full Text PDF PubMed Scopus (943) Google Scholar), namely Fatty Acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Sphingolipids (SP), and Sterols (ST). Annotation is modified to permit annotation of oxygenated lipids and examples will be given for lipid classes occurring outside the mammalian kingdom. “Biological intelligence” has been considered as topical knowledge about a lipid molecule, such as its structural building blocks, enzymatic pathways for generation and metabolism, and biological functions (4Liebisch G. Vizcaino J.A. Köfeler H. Trötzmüller M. Griffiths W.J. Schmitz G. Spener F. Wakelam M.J. Shorthand notation for lipid structures derived from mass spectrometry.J. Lipid Res. 2013; 54: 1523-1530Abstract Full Text Full Text PDF PubMed Scopus (463) Google Scholar). Interpretation by biological evidence in shorthand notation can be useful when mass spectra contain structural ambiguities or lack of clear structural evidence. Consequently, annotations with the help of biological evidence contain assumptions, and it must be recognized and recorded that this may lead to misinterpretations. Moreover, in the pragmatic approach presented in this work, we will make more use of common and/or trivial names for the shorthand notation. For example, the structures of sterols, prostaglandins, resolvins, etc. have been characterized by chemical and spectroscopic methods, including stereochemistry, and common names exist, as do shorthand notations in many cases. Their mass spectra are also known; however, their stereochemistry and isomerism and other structural information often cannot be deduced directly from the spectra when these lipids are measured in biological samples. Assignment of a common name or of shorthand notation to such chromatographic and MS/MS data is permissible, but it may be based on annotation that includes biological intelligence, and that needs to be clearly stated as well. In any case, assumptions made should be striking a unique balance between what we think we know about structure and function of a lipid molecule and what a specific MS-based analytical method definitively informs us about the lipid structure. Modification of Fatty Acyls by oxygen, either catalyzed enzymatically or by means of radical chemistry, is an important focus in biomedical research, due to the impressive biological activities of products thus obtained. Based on these two mechanisms, all compounds originating from polyunsaturated fatty acyls (PUFAs) having methylene-interrupted cis-double bonds (DBs) (also chemically referred to as allylic DBs) and being enzymatically or nonenzymatically oxygenated are grouped within the appropriate class in the Fatty Acyl category. Historically, the term “eicosanoid” has included “related oxygenated polyunsaturated fatty acids” with shorter or longer chain lengths, but in the LIPID MAPS classification, compounds are strictly assigned to a class based on their chain length (e.g., octadecanoids, eicosanoids, docosanoids). Recently, the common name “oxylipins”, standing for “oxygenated fatty acyls”, has come into widespread use. Similarly, in the Glycerophospholipids (GP) category, many newly described phospholipids contain oxygenated fatty acyls (or oxylipins) often termed “oxygenated phospholipids” (OxPLs). Those are produced by oxygenation of constituent fatty acyls enzymatically and nonenzymatically, or by chemical modification of polar head groups containing an amino function (PE and PS), i.e., N-modified phospholipids. In the following, we elaborate first on experimental prerequisites for correct annotation of lipid mass spectrometric data and, second, present the updates on rules for using shorthand notation. Finally, in order of categories, we present mostly in the form of easily readable tables, all updates on lipid nomenclature and classification including respective shorthand abbreviations according to the LIPID MAPS web resources and the updated shorthand notation for lipid species and lipid molecular species. To further enhance the understanding of shorthand notation, some chemical structures are presented in the tables. The updated shorthand notation schemes described herein have been incorporated into a number of key resources on the LIPID MAPS website, notably the LIPID MAPS Structure Database (LMSD) and the MS search tools (see the Hierarchical concept and application of shorthand notation section below), by generating level-specific abbreviations (e.g., sum-composition and chain-specific annotations) for lipid structures. This approach is important in terms of the development of MS search databases that are appropriate for the technique used (sum-composition databases for precursor ion data and chain-composition databases for MS/MS data). All lipid species and lipid molecular species data presented need information on levels of structural resolution attained by mass spectrometric analysis, and sufficient supplementary data to justify annotation by shorthand notation. At minimum, such data should contain the measured intact m/z value, the adduct ion used for identification, the retention time when chromatography is applied, and the measured fragment m/z values. Assignment and therefore use of specific shorthand nomenclature for defined functional groups (TABLE 1A, TABLE 1B, TABLE 1C) requires additional techniques. An example is derivatization of hydroxyl groups by trimethylsilylation followed by GC/MS EI and analysis of fragment ions formed. In many cases ESI-MS/MS of underivatized constituent fatty acyls in general leads to specific product ions, if ESI populates a charge site near the functional group (7Murphy R.C. Tandem Mass Spectrometry of Lipids: Molecular Analysis of Complex Lipids. Royal Molecular Society of Chemistry, Cambridge, UK2015Google Scholar). Definition of DB positions can be determined by several techniques including ozonolysis during analysis (OzID) (8Brown S.H. Mitchell T.W. Blanksby S.J. Analysis of unsaturated lipids by ozone-induced dissociation.Biochim. Biophys. Acta. 2011; 1811: 807-817Crossref PubMed Scopus (85) Google Scholar) or specific adduct formation with acetone in photochemical Paterno-Büchi reaction (9Ma X. Chong L. Tian R. Shi R. Hu T.Y. Ouyang Z. Xia Y. Identification and quantitation of lipid C=C location isomers: a shotgun lipidomics approach enabled by photochemical reaction.Proc. Natl. Acad. Sci. USA. 2016; 113: 2573-2578Crossref PubMed Scopus (165) Google Scholar). These reactions can be carried out in shotgun or LC-MS/MS experiments. High energy MS/MS has been used to assign DB position of fairly complex fatty acyls as well as methyl branching (10Cheng C. Gross M.L. Applications and mechanisms of charge-remote fragmentation.Mass Spectrom. Rev. 2000; 19: 398-420Crossref PubMed Scopus (214) Google Scholar). Alternatively, GC/MS can be used including specific derivatization of the carboxylate group, to drive specific DB fragmentation in EI spectra (11Harvey D.J. Picolinyl esters for the structural determination of fatty acids by GC/MS.Mol. Biotechnol. 1998; 10: 251-260Crossref PubMed Scopus (33) Google Scholar). Chemical ionization techniques are also useful by application of specific chemical ionization reagent gases to define DB positions (12Michaud A.L. Yurawecz M.P. Delmonte P. Corl B.A. Bauman D.E. Brenna J.T. Identification and characterization of conjugated fatty acid methyl esters of mixed double bond geometry by acetonitrile chemical ionization tandem mass spectrometry.Anal. Chem. 2003; 75: 4925-4930Crossref PubMed Scopus (58) Google Scholar).TABLE 1AAbbreviations of functional groups/side chainsFunctional Group/Side ChainAbbreviationEthyl branchEtMethyl branchMeBromoBrChloroClFluoroFIodoINitroNO2EpoxyEpPeroxyOOMethoxyOMeAlkoxy (ether)oxyAminoNH2HydroperoxyOOHSulfanylSHhydroxyOHOxo (keto/aldehyde; depending on position)oxoCyanoCNPhosphatePSulfateSCarboxylic acidCOOHGlycineGTaurineTThe order of functional groups aligns with IUPAC hierarchy (14Wilkinson I.M.S. IUPAC Commission on the Nomenclature of Organic Chemistry Panico R. Powell W.H. Richer J-C. A guide to IUPAC nomenclature of organic compounds: Recommendations 1993 (including revisions, published and hitherto unpublished, to the 1979 edition of Nomenclature of Organic Chemistry). Blackwell Scientific Publications, Oxford, UK1993Google Scholar). Open table in a new tab TABLE 1BAbbreviations of cyclic structuresCyclic StructuresAbbreviationCyclopropylcy3Cyclopropenylcy3:1Cyclobutylcy4Cyclopentylcy5Cyclohexylcy6 Open table in a new tab TABLE 1CAbbreviations of carbohydrate structuresCarbohydrate StructuresAbbreviationHexoseHexGalactoseGalGlucoseGlcMannoseManNeuraminic acidNeuN-acetyl hexosamineHexNAcN-acetyl galactosamineGalNAcN-acetyl glucosamineGlcNAcN-acetyl neuraminic acidNeuAcN-glycolylneuraminic acidNeuGcKeto-deoxy-glycero-galacto-nononic acidKdnGlucuronic acidGlcAXyloseXylFucoseFucGlycan annotation is based on IUPAC-approved abbreviations (https://www.ncbi.nlm.nih.gov/glycans/snfg.html) (15Neelamegham S. Aoki-Kinoshita K. Bolton E. Frank M. Lisacek F. Lütteke T. O'Boyle N. Packer N.H. Stanley P. Toukach P. et al.SNFG Discussion GroupUpdates to the symbol nomenclature for glycans guidelines.Glycobiology. 2019; 29: 620-624Crossref PubMed Scopus (80) Google Scholar). Open table in a new tab The order of functional groups aligns with IUPAC hierarchy (14Wilkinson I.M.S. IUPAC Commission on the Nomenclature of Organic Chemistry Panico R. Powell W.H. Richer J-C. A guide to IUPAC nomenclature of organic compounds: Recommendations 1993 (including revisions, published and hitherto unpublished, to the 1979 edition of Nomenclature of Organic Chemistry). Blackwell Scientific Publications, Oxford, UK1993Google Scholar). Glycan annotation is based on IUPAC-approved abbreviations (https://www.ncbi.nlm.nih.gov/glycans/snfg.html) (15Neelamegham S. Aoki-Kinoshita K. Bolton E. Frank M. Lisacek F. Lütteke T. O'Boyle N. Packer N.H. Stanley P. Toukach P. et al.SNFG Discussion GroupUpdates to the symbol nomenclature for glycans guidelines.Glycobiology. 2019; 29: 620-624Crossref PubMed Scopus (80) Google Scholar). Common names of lipid species, e.g., for certain fatty acids and for oxygenated fatty acids denote a chemically defined structure including stereochemistry. For proper annotations in these cases, the analytical method has to provide for chiral separation of known stereoisomeric compounds. This validation demands data on reproducibility and limit of quantification. Similarly, when novel structures are described, analytical details proving structural details need to accompany the data. Guidelines for method validation and reporting of novel lipid molecules are currently being developed within the Lipidomics Standard Initiative (https://lipidomics-standards-initiative.org) as community-wide effort (13Liebisch G. Ahrends R. Arita M. Arita M. Bowden J.A. Ejsing C.S. Griffiths W.J. Holcapek M. Köfeler H.C. Mitchell T.W. et al.Lipidomics Standards Initiative ConsortiumLipidomics needs more standardization.Nat. Metab. 2019; 1: 745-747Crossref PubMed Scopus (46) Google Scholar). Here, we describe updates and rules applicable to all lipid categories described below. This includes rules on the hierarchical concept and application of the nomenclature and annotation of lipid structures as well as on annotation of stable isotope-labeled lipids. Three major updates are: •The term “DBs” is replaced by “double bond equivalents” (DBEs), because removal of two hydrogen atoms from precursor lipid forms a double bond, an oxo group or a cyclic structure. Frequently, MS does not distinguish between these alternatives.•Oxygen atoms represent not only the main component introduced during oxygenation, but occurs also in hydroxy groups as a principal structural feature in many lipid classes such as sphingoid bases. Because hydroxy, oxo or other oxygen functional groups may not be differentiated by high resolution/accurate mass analysis, annotation is done by the number of oxygens linked to the hydrocarbon chain.•Use of parentheses and brackets is minimized. Parentheses indicate primarily positions and, with regard to functional groups only those with numbers behind them, like (OH)2, (NO2), (NH2). The use of square brackets is restricted to chemical configurations R and S, to stable isotopes, and to the frame of carbons in a ring structure. •Upon application of a validated MS-method, interpretation of mass spectra by “biological intelligence” and the use of common or trivial names, as alluded to specifically in the introduction, is permissible. Such annotations need to be clearly stated. Examples are ambiguities pertaining to bond type, oxygenated groups, and branched chains.•“Species level” is now the lowest hierarchical level. It represents the sum composition, i.e., sum of carbon atoms, DBEs, and number of additional oxygen atoms, e.g., FA 18:1;O. It thus replaces former “Lipid class level” mass (i.e., lipid class and the – uncharged - molecular mass). Of note, for sterols, the ABCD ring system is assumed and not expressed as DBE.•“Phosphate-position level” annotates positions of phosphate group(s), e.g., PIP(3′) or PIP2(4′,5′) at phosphatidylinositolphosphate.•“Molecular species level” pertains to all categories addressed here and is reached as soon as constituent fatty acyl/alkyl-residues are identified, e.g., TG 16:0_18:1_18:1, a triglyceride.•“sn-position level” is a more refined level in GL and GP categories, enabling annotation of the sn-position of fatty acyl/alkyl constituents at the glycerol backbone as indicated by a slash, e.g., TG 16:0/18:1/18:1.•“DB-position level” or “DBE-position level” pertain to species having constituents with defined position of double bonds or double bond equivalents, e.g., FA 18:2 (9, 11);O.•“Structure defined level” annotates molecular species composed of various constituents and functional groups, yet without positions and stereochemical details, e.g., FA 18:2;OH.•“Full structure level” annotates molecular species composed of various constituents and functional groups including positions, yet without stereochemical details, e.g., FA 18:2(9Z,11E);13OH.•“Complete structure level” defines detailed structures of all functional groups including stereochemistry as shown in the LMSD, e.g., 13R-HODE, 13S-HODE (= common name). Figure 1 presents such a hierarchical scheme, taking the example of glucosylceramide. A word of caution is appropriate here: Annotations based solely on m/z features and on returns from database retrieval are frequently incorrect due to over-interpretation of experimental data, i.e., returns of chemically defined lipid molecules at Complete structure level. It is therefore of major importance that database search tools return appropriate annotations based on sum composition, i.e., at Species level and Molecular species level. Such tools are, for example, the LIPID MAPS MS search tools (https://lipidmaps.org/resources/tools/bulk_structure_searches_overview.php) (see also comment in the discussion) or the “ALEX lipid calculator” (http://alex123.info/ALEX123/MS.php). •Lipid species are annotated by class shorthand abbreviation (see Tables 2A-6A), followed by a space and C-atoms:DBE, e.g., TG 54:5, or C-atoms:DBE;O-atoms in fatty acyl/alkyl residues, e.g., FA 18:1;O or PC 38:3;O2.TABLE 2AClass abbreviations in Category FACommon NameLipid Class, LIPID MAPSAbbreviationFatty acidsFatty acids and conjugates [FA01]FAFatty alcoholsFatty alcohols [FA05]FOHFatty aldehydesFatty aldehydes [FA06]FALAcyl carnitinesFatty acyl carnitines [FA0707]CARAcyl CoAsFatty acyl CoAs [FA0705]CoAN-acyl aminesN-acyl amines [FA0802]NAN-acyl ethanolaminesN-acyl ethanolamines (endocannabinoids) [FA0804]NAEN-acyl taurinesN-acyl amines [FA0802]NATWax estersWax monoesters [FA0701]WEWax diestersWax diesters [FA0702]WDFA estolidesFAHFA wax monoesters [FA0701]FA-EST Open table in a new tab •Variable constituents like fatty acyls/alkyls are assigned based on their mass as number of C-atoms and number of DBE (C-atoms:DBE), when experimental proof for DB is provided the annotation is C-atoms:DB. Where applicable, the number of oxygen-atoms is added, separated by a semi-colon, e.g., C-atoms:DBE;O-atoms.•DB-position is indicated by a number according to D -nomenclature (geometry unknown) or a number followed by geometry (Z for cis, E for trans). Specific techniques are required for determination of DB-position (or geometry) to validly use this level of annotation, e.g., FA 18:2 (9, 12), FA 18:2(9Z,12Z).•Positions for all functional groups are stated in front of functional group abbreviation, e.g., FA 20:4;12OH.•Generally, all functional groups (see for abbreviations) are separated by a semicolon after the number of DBE. Functional groups are placed inside a separate pair of parentheses, only if more than one followed by the number of groups, e.g., FA 20:3;(OH)2;oxo. Moreover, functional groups containing numbers such as NO2 or NH2 are generally placed inside a separate pair of parentheses, e.g., FA 18:1;(NO2). The order of functional groups follows the IUPAC hierarchy (14).•Except for DBE/DB-position, proven positions of all other functional groups are stated according to D -nomenclature in front of the functional group abbreviation that are separated by a comma if more than one, e.g., FA 20:3(5Z,13E);11OH,15OH;9oxo•Cyclic structures cyX (X = number of ring atoms, see for abbreviations) are presented in front of other functional groups. Their structural details are annotated within a pair of square brackets. Within the square brackets the positions of ring atoms, separated by hyphen, are placed in front of the cyX annotation. Other functional groups are placed after the ring structure of the cyX annotation, e.g., FA 20:2;[8-12cy5;11OH;9oxo];15OH = 8-iso-PGE2 or PGE2.•Carbohydrate structures (), e.g., in complex glycosphingolipids, are annotated as described for glycans (https://www.ncbi.nlm.nih.gov/glycans) (15). When the sequence of sugars components is known they are shown in this order separated by a hyphen, e.g., Gal-Glc-Cer 18:1;O2/16:0. In case the sequence is unknown the components (followed by their number if more than one) are shown in alphabetic order in front of the respective lipid backbone, e.g., Gal2GlcCer 18:1;O2/16:0.•Acyl-linkages (N- and/or O-) are annotated by FA C-atoms:DBE inside a separate pair of parentheses with proven position in front, e.g., Cer 18:1;O2/26:0;26O(FA 18:2).•Alkyl-linkages (N- and/or O-) are annotated by C-atoms:DBE inside a separate pair of parentheses with proven position in front, e.g., FA 18:1(12Z);9O(16:1) for an ether lipid.•When functional groups are part of lipid class abbreviation, e.g., PIP2 or SPBP, their proven positions are shown inside parentheses, separated by a comma if more than one, e.g., PIP2(4′,5′) 38:4 or SPBP (1) 18:1;O2.•Greek letters are transcribed to Latin letters as follows: α to a, β to b, γ to g, δ to d, ω to w.•Proven stereochemistry is shown after the respective functional group/side chain in square brackets [R] or [S], e.g., FA 20:4(6Z,8E,10E,14Z);5OH[S],12OH[R] = LTB4. •Isotope-containing lipid structures are indicated in square brackets annotating the isotope, followed by the number of isotopic atoms, e.g., FA 18:1[13C5].• Multiple isotopes are separated by a comma, e.g., FA 18:1[13C5,D4].•When positions of isotopes are known, they are indicated in a separate pair of parentheses in front of the isotope number, e.g., FA 18:1[(14,15,16,17,18)13C5].•Isotopes in fatty acyls or alkyls and in sphingoid bases are indicated in square brackets after the number of DBE, e.g., PC 34:1[D9] or PC O-16:0_18:1[13C5] and in Cer 34:1;O2[13C3], respectively. Isotopes in head groups of these structures are indicated in square brackets after class shorthand abbreviation, e.g., PC[D9] 34:1, TG[13C3] 54:3, SM[D9] 34:1;O2.•When positions of isotopes in the lipid are not known, they are indicated in square brackets in front of class shorthand abbreviation, e.g., [D5]PC 34:1, [13C7]TG 54:3. Shorthand abbreviations for Fatty Acyl classes are stated in Table 2A. Table 2B shows that lowest resolution level is based on m/z values, i.e., annotation at Species level (low mass resolution MS, e.g., carboxylate anion and oxygen atoms from functional groups). In addition, it is assumed that only a straight-chain fatty acid with or without DBE(s) is present. High mass resolution with accurate mass measurements may identify additional elements such as oxygen atoms of functional groups. Thus, a limited amount of structural information is provided at this level of analysis following the rules alluded to in the Annotation of lipid structures section, i.e., Species level. Annotation at DB-position level requires techniques such as ozonolysis (8Brown S.H. Mitchell T.W. Blanksby S.J. Analysis of unsaturated lipids by ozone-induced dissociation.Biochim. Biophys. Acta. 2011; 1811: 807-817Crossref PubMed Scopus (85) Google Scholar) or photochemical derivatization (9Ma X. Chong L. Tian R. Shi R. Hu T.Y. Ouyang Z. Xia Y. Identification and quantitation of lipid C=C location isomers: a shotgun lipidomics approach enabled by photochemical reaction.Proc. Natl. Acad. Sci. USA. 2016; 113: 2573-2578Crossref PubMed Scopus (165) Google Scholar) or GC-MS. The use of trivial or common names for even simple fatty acids implies that additional methods have been used to define the exact structure, such as a straight-chain, positions of DBs, or DB geometries. Chiral chromatography preceding MS/MS is required for respective stereochemistry. Because this is generally not routinely done, investigators should note in their reports when using a common name for a fatty acid that “The identity and stereochemistry of the fatty acid species reported using a common name (e.g., oleic acid, linolenic acid, arachidonic acid, etc.) is assumed based on biological intelligence”. This comment applies to simple as well as complex lipids that include fatty acids as part of the structure (e.g., glycerophospholipids, triacylglycerols, etc.). Examples for shorthand notation of fatty acids are presented in Table 2B.TABLE 2BLevel-dependent shorthand notation for examples of fatty acidsSubclassSpecies LevelaUncharged molecular mass measured by low resolution MS of corresponding m/z from carboxylate anion (electrospray ionization) or molecular ion species (radical cation by EI).,bAnnotation based on the assumption of a straight-chain fatty acyl plus functional groups based on exact mass measurements using a high-resolution mass spectrometer of fatty acyl indicating ion.DB-Position LevelcPositions of DBs determined by independent techniques such as ozonolysis (8) or photochemical derivatization (9).Full Structure LeveldShorthand notation applies only when exact location and nature of functional group(s) are determined by specific fragment ions obtained by derivatization and GC/MS or specific product ions in a MS/MS experiment.Complete Structure Level (= Common Name)eValidated assay is required to employ trivial names that engages appropriate internal standard, proper assessment of signal-to-noise, and a chromatographic based separation of potential isomers (GC or HPLC).Straight-chain FAFA 12:0LaurateFA 14:0MyristateFA 16:0PalmitateFA 16:1FA 16:1(9Ma X. Chong L. Tian R. Shi R. Hu T.Y. Ouyang Z. Xia Y. Identification and quantitation of lipid C=C location isomers: a shotgun lipidomics approach enabled by photochemical reaction.Proc. Natl. Acad. Sci. USA. 2016; 113: 2573-2578Crossref PubMed Scopus (165) Google Scholar)FA 16:1(9Z)PalmitoleateFA 18:0StearateFA 18:1FA 18:1(9Ma X. Chong L. Tian R. Shi R. Hu T.Y. Ouyang Z. Xia Y. Identification and quantitation of lipid C=C location isomers: a shotgun lipidomics approach enabled by photochemical reaction.Proc. Natl. Acad. Sci. USA. 2016; 113: 2573-2578Crossref PubMed Scopus (165) Google Scholar)FA 18:1(9Z)OleateFA 18:1FA 18:1(11Harvey D.J. Picolinyl esters for the structural determination of fatty acids by GC/MS.Mol. Biotechnol. 1998; 10: 251-260Crossref PubMed Scopus (33) Google Scholar)FA 18:1(11E)trans-" @default.
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• W3091953196 title "Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures" @default.
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