Abstract
Motivation: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage and signaling. Cellular lipidomes may contain tens of thousands of structures, a staggering degree of complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide a means to study this complexity, but the interpretation of lipidomic data and its integration with prior knowledge of lipid biology suffers from a lack of appropriate tools to manage the data and extract knowledge from it.Results: To facilitate the description and exploration of lipidomic data and its integration with prior biological knowledge, we have developed a knowledge resource for lipids and their biology—SwissLipids. SwissLipids provides curated knowledge of lipid structures and metabolism which is used to generate an in silico library of feasible lipid structures. These are arranged in a hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. SwissLipids provides a reference namespace for lipidomic data publication, data exploration and hypothesis generation. The current version of SwissLipids includes over 244 000 known and theoretically possible lipid structures, over 800 proteins, and curated links to published knowledge from over 620 peer-reviewed publications. We are continually updating the SwissLipids hierarchy with new lipid categories and new expert curated knowledge.Availability: SwissLipids is freely available at http://www.swisslipids.org/.Contact: alan.bridge@isb-sib.chSupplementary information: Supplementary data are available at Bioinformatics online.
Highlights
Lipids are a large and diverse group of biological molecules that perform a wide variety of biological functions (Sud et al, 2007)
Other resources and tools for the analysis of lipidomic data include LipidBLAST, which provides a library of 120 000 lipid structures and associated theoretical tandem mass spectra (Kind et al, 2013), LipidHome, a database of over 36 million hypothetical glycerolipid and glycerophospholipid structures designed for mass spectrometry (MS) data integration (Foster et al, 2013) and Visualization and phospholipid identification (VaLID) which provides a search engine for a library of hypothetical glycerophospholipid structures somewhat similar to those of LipidHome (Blanchard et al, 2013)
SwissLipids includes over 2000 curated enzymatic reactions which directly link more than 800 proteins (UniProtKB) and 1500 reactions (Rhea) and supporting evidence
Summary
Lipids are a large and diverse group of biological molecules that perform a wide variety of biological functions (Sud et al, 2007). Lipidome composition may be analyzed using mass spectrometry (MS) and tandem mass spectrometry (MS/MS)-based approaches which are able to quantify hundreds of lipid species over a broad dynamic range (da Silveira Dos Santos et al, 2014). These approaches provide information on the atomic composition of intact lipids and their component parts (such as acyl chains) which can be mapped to prior knowledge of lipid structures using a standardized hierarchical notation (Liebisch et al, 2013). KEGG has been used as basis for computational approaches for matching hypothetical structures to pathways (Yetukuri et al, 2007), these knowledge resources do not aim to provide comprehensive coverage of the hundreds of thousands of lipids that may exist in nature.
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