Mechanisms of lipid biosynthesis. Biosynthesis of ketoacyl- and isoprene-containing lipids proceeds by carbanion and carbocation-mediated chain extension, respectively.⁸

Overview of LIPID MAPS structure data generation methodology. Starting from specified abbreviations for lipids corresponding to LIPID MAPS format, the structure generation tools select an appropriate lipid structure template internally stored in MDL MOL file format, attach appropriate radyl chains, enumerate appropriate lipid structures and generate a MDL MOL structure file or SDF file containing structural data along with name and other ontology data (Reprinted with permission from Reference 13. Copyright 2007 Oxford University Press).

Overview of LIPID MAPS ontology data generation methodology from structure data.

Description of the LIPID MAPS LM ID.

A selection of screen shots showing various options for searching the LIPID MAPS Structure Database (LMSD) and result summary for a specific LM ID.

Overview of the bioinformatics process for creating the LIPID MAPS Proteome Database (LMPD).

Treatment module of LIMS (Reprinted with permission from Reference 57. Copyright 2007 Elsevier Limited).

A montage of screen shots showing LIPID MAPS mass spectroscopy tools.

Schema for online data display of timecourse results.

VANTED application showing the mouse arachidonate pathway and timecourse data mapped in heatmap format displayed under the lipid and enzyme (gene) nodes.

Identification of NF-κB, ISRE and AP-1/ATF/CREB binding sites in KLA-stimulated genes in RAW macrophages. Blue color indicates significant enrichment of the motif in promoters of positively regulated genes for each time point.

Heat map for the data for eicosanoids (measured in the media) and eicosanoid biosynthesis related genes (Reprinted with permission from Reference 2. Copyright 2010 American Society for Biochemistry and Molecular Biology). The four panels correspond to: (1) Data based on ratio of values for treatment with KLA to the values for control experiments, (2) ratio of compactin treatment to control, (3) ratio of treatment with both KLA and compactin to control, and (4) ratio data from (1)–(3) combined. The data in each row is scaled and offset by the t = 0 value. The names of the lipids/genes displayed on the y- and/or x-axis are listed in different colors to indicate the clusters.

Simulation of kinetic modeling of simplified lipid network: fit of the predicted response (control and treatment with KLA) to the corresponding experimental data. In the legend, ‘Ctrl’ refers to control and ‘Trt’ refers to KLA treatment of RAW264.7 cells. The error-bars shown on the experimental data are standard-error of mean (Reprinted with permission from Reference 129. Copyright 2009 Elsevier Limited).

Overview of the process of performing a quantitative lipid analysis of macrophage cell sample (in this example, a time-course experiment using bone marrow derived macrophages). Extraction methods, LC/GC purification methods, MS acquisition strategies and quantitative standard approaches are optimized for each lipid class.^2,70,72

Representative structures from each lipid category shown with LM ID, category name, category abbreviation, and systematic name (Reprinted with permission from Reference 10. Copyright 2007 Oxford University Press).

A montage of screen shots showing LIPID MAPS structure drawing tools. The top left box shows structure drawing tools available on the LIPID MAPS website. The top right box shows options available for generating a fatty acyl structure starting from either a complete abbreviation or individual specification of chain and substituent from a with its position and stereochemistry. The middle box shows an example of structure generation using acyl chains and head groups for glycerophospholipids. A comprehensive list of commonly occurring acyl chains and head groups is provided as a pull down list. The button box shows an example of a structure generated for a glycerophospholipid along with other ontological information.

Overview of LIPID MAPS Structure Database (LMSD) generation methodology.

Entity relationship diagram for LMSD showing the Oracle database tables containing structural and classification information as well as annotations and ontological data. The unique LM_ID identifier plays a central role as a primary key in this relational schema.

Entity relationship diagram for LMPD showing the Oracle database tables containing information pertaining to lipid-related genes and proteins for human and mouse species.

Main user interface of LIPID MAPS LIMS (Reprinted with permission from Reference 57. Copyright 2007 Elsevier Limited).