A simple online interface has been developed to enable an end-user to rapidly generate a variety of lipid chemical structures, along with corresponding systematic names and ontological information. The user interface is implemented using a combination of Perl and PHP scripts.
The fatty acyl structure-drawing tools support the specification of any valid fatty acyl LIPID MAPS abbreviation representing acyl chain length along with the specification of double bonds, triple bonds and a variety of substituents on the acyl chain. Alternatively, the user can also choose desired substituents for up to three positions on the acyl chain from the pull-down menus. Currently, the following substituents are supported: hydroxyl –OH, amino –NH2, thio - SH, methyl –Me, ethyl –Et, propyl –Pr, methoxy –OMe, acetoxy –OAc, keto/oxo –Ke, epoxy –Ep, methylene –My, hydroperoxy –OOH, bromo –Br, chloro –Cl, fluoro –F, cyano –CN, carboxy –COOH, aldehyde –CHO, and methyl ester – COOMe.
The glycerolipid structure-drawing tools provide the capability to generate a variety of monoradyl, diradyl and triradyl glycerols by specification of acyl chains at sn1
3 positions. After the user chooses the acyl chain abbreviation for different positions from the pull-down lists, the corresponding lipid structure is generated. Over 50 different acyl chain abbreviations are available for sn1
3 positions. Acyl chain abbreviation of 0:0
at the sn3
positions are used to generate structures for diradyl and monoradyl glycerols.
The cardioplipin structure-drawing tools also provide a pull-down list of acyl chain abbreviations to choose for positions sn1(1’), sn2(1’), sn1(3’), and sn2(3’). Except for the absence of acyl chain abbreviation of 0:0, this list is similar to the list of acyl chain abbreviations for glycerolipids. After the user chooses desired acyl chain abbreviations for all the four positions, the corresponding cardiolipin structure is generated.
The glycerophospholipid structure-drawing tools, in addition to pull-down list of acyl chain abbreviations for sn1
position also provide a pull-down list for various headgroups. Except for the absence of acyl chain abbreviation of 0:0
at sn1 position, this list is similar to the list of acyl chain abbreviations for glycerolipids. The following headgroup abbreviations are supported: GPCho (glycerophosphocholines), GPSer (glycerophosphoserines), GPEtn (glycerophosphoethanolamines), GPA (glycerophosphates), GPGro (glycerophosphoglycerols) and GPIns (glycerophosphoinositols).
The sphingolipid structure-drawing tools support the generation of a wide variety of sphingolipid structures by providing pull-down lists for sphingoid base, N-acyl group and headgroups. Supported sphingoid bases are: sphingosine, sphinganine, C16 sphingosine, C16 sphinganine, C17 sphingosine, C17 sphinganine, C19 sphingosine and C19 sphinganine. N-acyl group pull-down list contains the following acyl chain abbreviations: 0:0, 10:0, 12:0, 14:0, 16:0, 18:0, 20:0, 22:0, 24:0, 24:1(5Z), 26:0, and 26:1(17Z). The supported headgroups are: sphingomyelin, ceramide, ceramide-1-phosphate, and glucosyl ceramide.
The sterol-drawing tools support the generation of structures derived from cholestane sterol core. In addition to double bond position specification, the user can choose to substitute atoms in the cholestane core by C, N, O and H along with the stereochemistry specification of alpha or beta for the substituted atom. Pull-down lists for position, stereochemistry and atom specification are provided for up to four simultaneous substitutions.
MS prediction tools
The MS prediction tools for glycerolipids, cardiolipins and glycerophospholipids accept an m/z value from the user for the precursor ion and have a menu to allow selection of the ion mode ([M+H]+, [M+NH4]+, [M-H]−, etc). In addition, a mass tolerance range and a headgroup (in the case of glycerophospholipids) may be specified to limit the number of matches. The list of matches may also be filtered by specifying a particular chain, using the LIPID MAPS abbreviation format. On completion of a search, the output format () contains a list of structures that (a) satisfy the input criteria and (b) whose side chains belong to the list (48 in the case of glycerolipids and glycerophospholipids, 10 in the case of cardiolipins) of radyl chains used to populate the database. The predicted masses of the fragment ions are computed at run-time by the online application. All entries in the result set are hyperlinked to the structure-drawing application (under the ‘Abbreviation’ column), enabling ‘on-demand’ visualization of the molecular structures. Isotopic distribution profiles for each structure may also be viewed under the ‘Formula’ column.
Online MS prediction tools for glycerophospholipids.