Bulk" Structure Searches — Documentation

Creation of the LIPID MAPS® Database of computationally-generated "bulk" Lipid Species (COMP_DB)

The LIPID MAPS® Database of computationally-generated "bulk" Lipid Species (COMP_DB) is a virtual database composed of major classes of lipid species, generated from list of commonly occurring acyl/alkyl chains (see below) These "bulk" lipid species indicate the number of carbons and number of "double bond equivalents" (DBE), but not chain positions or double bond regiochemistry and geometry. The concept of a double bond equivalent unites a range of chemical functionality which gives rise to isobaric features by mass spectometry. For example a chain containing a ring results in loss of 2 hydrogen atoms (compared to a linear structure) and thus has 1 DBE since the mass and molecular formula is identical to a linear structure with one double bond. Similarly, conversion of a hydroxyl group to ketone results in loss of 2 hydrogen atoms, therefore the ketone is assigned 1 DBE. Where applicable, the number of oxygen atoms is added to the abbreviation, separated by a semi-colon. Oxygen atoms in the class-specific functional group (e.g. the carboxylic acid group for fatty acids or the phospholcholine group for PC) are excluded. In the case of sphingolipids, all oxygen atoms apart from the amide oxygen are included, in order to discrminate, for example, between 1-deoxyceramides (O), ceramides (O2) and phytoceramides (O3). A comprehensive list of examples is shown below.

  • Fatty acyls
    • Fatty acids/esters (FA) Example:C20H34O5 => FA 20:3;O3
    • Acyl carnitines (CAR) Example:C15H29NO4 => CAR 8:0
    • Acyl CoAs (CoA) Example:C35H62N7O18P3S => CoA 14:0;O
    • N-acyl ethanolamines (NAE) Example:C22H37NO2 => NAE 20:4
    • N-acyl taurines (NAT) Example:C20H39NO4S => NAT 18:1
  • Glycerolipids
    • Monoradylglycerols
      • Monoacylglycerols (MG) Example:C19H38O4 => MG 16:0
      • Monoalkylglycerols (MG O) Example:C19H40O3 => MG O-16:0
    • Diradylglycerols
      • Diacylglycerols (DG) Example:C35H68O => DG 32:0
      • Alkylacylglycerols (DG O) Example:C35H70O4 => DG O-32:0
    • Triradylglycerols
      • Triacylglycerols (TG) Example:C51H98O6 => TG 48:0
      • Alkyldiacylglycerols (TG O) Example:C51H100O5 => TG O-48:0
  • Glycerophospholipids
    • Glycerophosphocholines
      • Diacylglycerophosphocholines (PC) Example:C42H84NO8P => PC 34:0
      • Alkylacylglycerophosphocholines (PC O) Example:C42H86NO7P => PC O-34:0
      • Monoacylglycerophosphocholines (LPC) Example:C24H50NO7P => LPC 16:0
      • Monoalkylglycerophosphocholines (LPC O) Example:C24H52NO6P => LPC O-16:0
    • Glycerophosphoethanolamines
      • Diacylglycerophosphoethanolamines (PE) Example:C37H68NO9P => PE 32:3;O
      • Alkylacylglycerophosphoethanolamines (PE O) Example:C37H70NO8P => PE O-32:3;O
      • Monoacylglycerophosphoethanolamines (LPE) Example:C29H58NO7P => LPE 24:1
      • Monoalkylglycerophosphoethanolamines (LPE O) Example:C29H60NO6P => LPE O-24:1
    • Glycerophosphoethanoserines
      • Diacylglycerophosphoserines (PS) Example:C40H72NO10P => PS 34:3
      • Alkylacylglycerophosphoserines (PS O) Example:C40H74NO9P => PS O-34:3
      • Monoacylglycerophosphoserines (LPS) Example:C24H46NO9P => LPS 18:1
      • Monoalkylglycerophosphoserines (LPS O) Example:C24H48NO8P => LPS O-18:1
    • Glycerophosphoglycerols
      • Diacylglycerophosphoglycerols (PG) Example:C34H67O10P => PG 28:0
      • Alkylacylglycerophosphoglycerols (PG O) Example:C34H69O9P => PG O-28:0
      • Monoacylglycerophosphoglycerols (LPG) Example:C24H45O9P => LPG 18:2
      • Monoalkylglycerophosphoglycerols (LPG O) Example:C24H49O8P => LPG O-18:1
      • Bis-(monoacylglycerol)phosphates (BMP) Example:C40H75O10P => BMP 34:2
    • Glycerophosphoinositols
      • Diacylglycerophosphoinositols (PI) Example:C41H79O13P => PI 32:0
      • Alkylacylglycerophosphoinositols (PI O) Example:C41H79212P => PI O-32:0
      • Monoacylglycerophosphoinositols (LPI) Example:C29H55O12P => LPI 20:1
      • Monoalkylglycerophosphoinositols (LPI O) Example:C29H57O11P => LPI O-20:1
    • Glycerophosphates
      • Diacylglycerophosphates (PA) Example:C39H77O8P => PA 36:0
      • Alkylacylglycerophosphates (PA O) Example:C39H79O7P => PA O-36:0
      • Monoacylglycerophosphates (LPA) Example:C21H39O7P => LPA 18:2
      • Monoalkylglycerophosphates (LPA O) Example:C21H43O6P => LPA O-18:1
    • Glycerophosphoinositol phosphates
      • Diacylglycerophosphoinositol phosphates (PIP) Example:C43H82O16P2 => PIP 34:1
    • Glycerophosphoinositol bisphosphates
      • Diacylglycerophosphoinositol bisphosphates (PIP2) Example:C46H83O19P3 => PIP2 37:4
    • Glycerophosphoinositol trisphosphates
      • Diacylglycerophosphoinositol trisphosphates (PIP3) Example:C46H84O22P4 => PIP3 37:4
    • Glycerophosphoglycerophosphoglycerols
      • (Tetraacyl)Cardiolipins (CL) Example:C73H142O17P2 => CL 64:0
  • Sphingolipids
    • Sphingoid bases
      • Sphingoid bases (SPB) Example:C18H37NO2 => SPB 18:1;O2
      • Sphingoid base phosphates (SPBP) Example:C18H40NO6P => SPBP 18:0;O3
    • Ceramides
      • Ceramides (Cer) Example:C34H67NO3 => Cer 34:1;O2
      • Acyl Ceramides (ACer) Example:C56H109NO4 =>ACer 56:1;O2
      • Ceramide phosphates (CerP) Example:C42H82NO6P => CerP 42:2;O2
    • Phosphosphingolipids
      • Sphingomyelins (SM) Example:C39H79N2O6P => SM 34:1;O2
      • PE ceramides (PE-Cer) Example:C38H73N2O6P => EPC 36:3;O2
      • PI ceramides (PI-Cer) Example:C48H96NO13P => IPC 42:0;O4
      • Mannosyl-PI-ceramides (MIPC) Example:C54H106NO18P => MIPC 42:0;O4
      • Mannosyl-di-PI-ceramides (M(IP)2C) Example:C60H117NO26P2 => M(IP)2C 42:0;O4
    • Glycosphingolipids
      • Neutral glycosphingolipids
        • Hexosyl ceramides (HexCer) Example:C40H77NO8 => HexCer 34:1;O2
        • Dihexosyl ceramides (Hex2Cer) Example:C46H87NO13 => Hex2Cer 34:1;O2
      • Acidic glycosphingolipids
        • Sulfatides (SHexCer) Example:C40H77NO11S => SHexCer 34:1;O2
  • Sterol lipids
    • Sterols, inc. bile acids (ST) Example:C24H40O5 => ST 24:1;O5
    • Cholesterol esters (CE) Example:C43H76O2 => CE 16:0
    • Sterol conjugates
      • Sterol Glycine conjugates (ST;G) Example:C26H43NO6 => ST 24:1;O5;G
      • Sterol Taurine conjugates (ST;T) Example:C26H45NO7S => ST 24:1;O5;T
      • Sterol Sulfate conjugates (ST;S) Example:C24H40O6S => ST 24:1;O3;S
      • Sterol Glucuronic acid conjugates (ST;GlcA) Example:C30H48O11 => ST 24:1;O5;GlcA
      • Sterol Hexose conjugates (ST;Hex) Example:C33H56O6 => ST 27:1;O;Hex
      • Sterol N-acetyl-hexosamine conjugates (ST;HexNAc) Example:C35H59NO6 => ST 27:1;O;HexNAc
      • Sterol multiple conjugates (ST;[G;GlcA;Hex;HexNAc;S;T]) Example:C26H43NO7S (Glycolithocholic acid sulfate)=> ST 24:1;O3;G;S

    • Commonly occurring acyl/alkyl chains used to create COMP_DB

    The acyl/alkyl chains used to create the COMP_DB database of glycerophospholipids, glycerolipids, sphingolipids, acyl carnitines, acyl CoA's, cholesteryl esters and wax esters:
    10:0 12:0 13:0 14:0 14:1 15:0 15:1 16:0 16:1 17:0 17:1 17:2 18:0 18:1 18:2 18:3 18:4 19:0 20:0 20:1 20:2 20:3 20:4 20:5 21:0 22:0 22:1 22:2 22:4 22:5 22:6 23:0 24:0 24:1 24:2 24:3 24:4 24:5 25:0 25:1 26:0 26:1 26:2 26:3 26:4 26:5 26:6 27:0 27:1 27:3 28:0 28:1 28:2 28:3 28:4 28:5 28:6 29:0 29:2 29:3 30:0 30:1 30:2 30:3 30:4 30:5 30:6 31:0 32:0 32:1 32:4 32:5 32:6 33:0 34:0 34:4 34:5 34:6 O-16:0 O-18:0 O-20:0 P-16:0 P-18:0 P-20:0

    The acyl chains used to create the COMP_DB database of fatty acids: (OH:hydroxyl, Ke: keto(oxo), Ep:epoxy)
    (only searched in negative ion mode) 10:0 10:1 10:2 10:3 10:4 10:5 11:0 11:1 11:2 11:3 11:4 11:5 12:0 12:1 12:2 12:3 12:4 12:5 12:6 13:0 13:1 13:2 13:3 13:4 13:5 13:6 14:0 14:1 14:2 14:3 14:4 14:5 14:6 15:0 15:1 15:2 15:3 15:4 15:5 15:6 16:0 16:1 16:2 16:3 16:4 16:5 16:6 17:0 17:1 17:2 17:3 17:4 17:5 17:6 18:0 18:1 18:2 18:3 18:4 18:5 18:6 19:0 19:1 19:2 19:3 19:4 19:5 19:6 20:0 20:1 20:2 20:3 20:4 20:5 20:6 21:0 21:1 21:2 21:3 21:4 21:5 21:6 22:0 22:1 22:2 22:3 22:4 22:5 22:6 23:0 23:1 23:2 23:3 23:4 23:5 23:6 24:0 24:1 24:2 24:3 24:4 24:5 24:6 25:0 25:1 25:2 25:3 25:4 25:5 25:6 26:0 26:1 26:2 26:3 26:4 26:5 26:6 27:0 27:1 27:2 27:3 27:4 27:5 27:6 28:0 28:1 28:2 28:3 28:4 28:5 28:6 29:0 29:1 29:2 29:3 29:4 29:5 29:6 30:0 30:1 30:2 30:3 30:4 30:5 30:6 31:0 31:1 31:2 31:3 31:4 31:5 31:6 32:0 32:1 32:2 32:3 32:4 32:5 32:6 33:0 33:1 33:2 33:3 33:4 33:5 33:6 34:0 34:1 34:2 34:3 34:4 34:5 34:6

    The acyl chains used to create the COMP_DB database of cardiolipins:
    12:0 14:0 14:1 16:0 16:1 18:0 18:1 18:2 18:3 20:0 20:1 20:2 20:3 20:4 20:5 22:0 22:1 22:2 22:4 22:5 22:6 24:0 24:1 26:0 26:1