LIPID MAPS online tools for lipid research

LIPID MAPS Bioinformatics Core, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA.
Nucleic Acids Research (Impact Factor: 9.11). 08/2007; 35(Web Server issue):W606-12. DOI: 10.1093/nar/gkm324
Source: PubMed

ABSTRACT The LIPID MAPS consortium has developed a number of online tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry (MS) data. 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 structure-drawing tools are available for six categories of lipids: (i) fatty acyls, (ii) glycerolipids, (iii) glycerophospholipids, (iv) cardiolipins, (v) sphingolipids and (vi) sterols. Within each category, the structure-drawing tools support the specification of various parameters such as chain lengths at a specific sn position, head groups, double bond positions and stereochemistry to generate a specific lipid structure. The structure-drawing tools have also been integrated with a second set of online tools which predict possible lipid structures from precursor-ion and product-ion MS experimental data. The MS prediction tools are available for three categories of lipids: (i) mono/di/triacylglycerols, (ii) glycerophospholipids and (iii) cardiolipins. The LIPID MAPS online tools are publicly available at

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Available from: Shankar Subramaniam, May 25, 2015
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    • "Current structural libraries for glycolipids are limited in size. Partial tandem mass spectra libraries for glycolipids are available from LipidMaps (Dennis et al., 2005; Fahy et al., 2007). Dallas recently published a library of endogenous human milk peptides (Dallas et al., 2013a,b). "
    Encyclopedia of Agriculture and Food Systems, Edited by Van Alfen NK, 07/2014: chapter Determining Functional Properties and Sources of Recently Identified Bioactive Food Components: Oligosaccharides, Glycolipids, Glycoproteins, and Peptides: pages 441-461; Academic Press., ISBN: 978-0-08-093139-5
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    • "The AbsoluteIDQ™ p180 assay enables the detection of 186 metabolites including: 40 acylcarnitines (free carnitine – C0 and acylcarnitines – Cx:y), 21 amino acids, 19 biogenic amines, 90 glycerophospholipids including lysophosphatidylcholines (LysoPC a Cx:y) and phosphatidylcholines with acyl (PC aa Cx:y) or ether (PC ae Cx:y) side chain, hexoses (H1) and 15 sphingolipids (SM Cx:y). As previously described [25,26], the nomenclature used for lipid metabolites refers to the Lipid Maps comprehensive classification system [27]. The nomenclature for lipids is as follows: Cx:y, where “x” denotes the number of carbons (C) and “y” represents the number of double bonds. "
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    ABSTRACT: High-throughput screening techniques that analyze the metabolic endpoints of biological processes can identify the contributions of genetic predisposition and environmental factors to the development of common diseases. Studies applying controlled physiological challenges can reveal dysregulation in metabolic responses that may be predictive for or associated with these diseases. However, large-scale epidemiological studies with well controlled physiological challenge conditions, such as extended fasting periods and defined food intake, pose logistic challenges. Culturally and religiously motivated behavioral patterns of life style changes provide a natural setting that can be used to enroll a large number of study volunteers. Here we report a proof of principle study conducted within a Muslim community, showing that a metabolomics study during the Holy Month of Ramadan can provide a unique opportunity to explore the pre-prandial and postprandial response of human metabolism to nutritional challenges. Up to five blood samples were obtained from eleven healthy male volunteers, taken directly before and two hours after consumption of a controlled meal in the evening on days 7 and 26 of Ramadan, and after an over-night fast several weeks after Ramadan. The observed increases in glucose, insulin and lactate levels at the postprandial time point confirm the expected physiological response to food intake. Targeted metabolomics further revealed significant and physiologically plausible responses to food intake by an increase in bile acid and amino acid levels and a decrease in long-chain acyl-carnitine and polyamine levels. A decrease in the concentrations of a number of phospholipids between samples taken on days 7 and 26 of Ramadan shows that the long-term response to extended fasting may differ from the response to short-term fasting. The present study design is scalable to larger populations and may be extended to the study of the metabolic response in defined patient groups such as individuals with type 2 diabetes.
    Journal of Translational Medicine 06/2014; 12(1):161. DOI:10.1186/1479-5876-12-161 · 3.93 Impact Factor
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    • "Multivariate data analysis (MVDA) was used to extract the relevant underlying information in large mass spectrometry (MS) data sets. The metabolite identification of the selected features was performed by comparing the marker exact mass with the exact mass of the potential biomarker in different databases [28] [29] with a given mass range (±5 ppm). The MS/MS spectra of the possible compounds and standard solutions, whenever possible, were used to confirm the identification of the potential biomarkers. "
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    ABSTRACT: Early allograft dysfunction (EAD) dramatically influences graft and patient outcome after orthotopic liver transplantation and its incidence is strongly determined by donor liver quality. Nevertheless, objective biomarkers, which can assess graft quality and anticipate organ function, are still lacking. This study aims to investigate whether there is a preoperative donor liver metabolomic biosignature associated with EAD. A comprehensive metabolomic profiling of 124 donor liver biopsies collected before transplantation was performed by mass spectrometry coupled to liquid chromatography. Donor liver grafts were classified into two groups: showing EAD and immediate graft function (IGF). Multivariate data analysis was used to search for the relationship between the metabolomic profiles present in donor livers before transplantation and their function in recipients. A set of liver graft dysfunction-associated biomarkers was identified. Key changes include significantly increased levels of bile acids, lysophospholipids, phospholipids, sphingomyelins and histidine metabolism products, all suggestive of disrupted lipid homeostasis and altered histidine pathway. Based on these biomarkers, a predictive EAD model was built and further evaluated by assessing 24 independent donor livers, yielding 91% sensitivity and 82% specificity. The model was also successfully challenged by evaluating donor livers showing primary non-function (n=4). A metabolomic biosignature that accurately differentiates donor livers, which later showed EAD or IGF, has been deciphered. The remarkable metabolomic differences among between donor livers before transplant can relate to their different quality. The proposed metabolomic approach may become a clinical tool for donor liver quality assessment and for anticipating graft function before transplant.
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