A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

Herzog, Ronny; Schwudke, Dominik; Schuhmann, Kai; Sampaio, Júlio L.; Bornstein, Stefan R.; Schroeder, Michael; Shevchenko, Andrej

doi:10.1186/gb-2011-12-1-r8

Cited by 372 publications

(333 citation statements)

References 44 publications

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“…Data Processing-Lipids were identified by LipidXplorer software by matching m/z of their monoisotopic peaks to the corresponding elemental composition constraints (36).…”

Section: Lipidomics Analysismentioning

confidence: 99%

Stimulation, Inhibition, or Stabilization of Na,K-ATPase Caused by Specific Lipid Interactions at Distinct Sites

Habeck¹,

Haviv²,

Katz³

et al. 2015

Journal of Biological Chemistry

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Background: Na,K-ATPase is stabilized by phosphatidylserine/cholesterol and is stimulated by neutral phospholipids. Results: Three specific lipid-Na,K-ATPase interactions are detectable that either (a) stabilize the protein or (b) stimulate or (c) inhibit Na,K-ATPase activity, with distinct kinetic mechanisms. Conclusion: There are separate binding sites for phosphatidylserine/cholesterol (stabilizing), polyunsaturated phosphatidylethanolamine (stimulatory), and sphingomyelin/cholesterol (inhibitory). Significance: In physiological conditions, specifically bound lipids may regulate Na,K-ATPase activity.

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“…Data Processing-Lipids were identified by LipidXplorer software by matching m/z of their monoisotopic peaks to the corresponding elemental composition constraints (36).…”

Section: Lipidomics Analysismentioning

confidence: 99%

Stimulation, Inhibition, or Stabilization of Na,K-ATPase Caused by Specific Lipid Interactions at Distinct Sites

Habeck¹,

Haviv²,

Katz³

et al. 2015

Journal of Biological Chemistry

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“…Molecular lipid species were identified and quantified using LipidXplorer software (17) developed by MPI CBG (Dresden, Germany). Species were quantified by comparing the intensities of their peaks to peaks of spiked internal standards; lipid quantities determined in individual samples were normalized by the total protein content determined by Bradford assay.…”

Section: Liver Lipidomicsmentioning

confidence: 99%

Liver-Restricted Repin1 Deficiency Improves Whole-Body Insulin Sensitivity, Alters Lipid Metabolism, and Causes Secondary Changes in Adipose Tissue in Mice

et al. 2014

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Replication initiator 1 (Repin1) is a zinc finger protein highly expressed in liver and adipose tissue and maps within a quantitative trait locus (QTL) for body weight and triglyceride (TG) levels in the rat. The QTL has further been supported as a susceptibility locus for dyslipidemia and related metabolic disorders in congenic and subcongenic rat strains. Here, we elucidated the role of Repin1 in lipid metabolism in vivo. We generated a liver-specific Repin1 knockout mouse (LRep1 2/2 ) and systematically characterized the consequences of Repin1 deficiency in the liver on body weight, glucose and lipid metabolism, liver lipid patterns, and protein/mRNA expression. Hyperinsulinemic-euglycemic clamp studies revealed significantly improved wholebody insulin sensitivity in LRep1 2/2 mice, which may be due to significantly lower TG content in the liver. Repin1 deficiency causes significant changes in potential downstream target molecules including Cd36, Pparg, Glut2 protein, Akt phosphorylation, and lipocalin2, Vamp4, and Snap23 mRNA expression. Mice with hepatic deletion of Repin1 display secondary changes in adipose tissue function, which may be mediated by altered hepatic expression of lipocalin2 or chemerin.Our findings indicate that Repin1 plays a role in insulin sensitivity and lipid metabolism by regulating key genes of glucose and lipid metabolism.Previously, we identified a quantitative trait locus (QTL) for body weight, serum fasting insulin, and triglycerides (TGs) on rat chromosome 4 (1-3). Replication initiator 1 (Repin1) emerged as a potential positional candidate gene within the QTL region considering associations of metabolic alterations in rats with a single nucleotide polymorphism (449C/T) in the Repin1 coding region and with the size of a triplet repeat in the 39-untranslated region of the Repin1 gene (4). Repin1 was initially discovered as replication initiation region protein 60 kDa (RIP60) in a study investigating DNA binding proteins involved in replication activation of the Chinese hamster dihydrofolate reductase gene (dhfr) (5). Repin1 binds to two ATT-rich sites in orib, a short region 39 to the dhfr gene, acting as an enhancer of DNA bending during initiation of DNA synthesis (6,7). Plasmid replication assays demonstrated

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“…The low abundant precursors are often not fragmented in all acquisitions and often occur with non-equal efficiency. The peak occupancy attribute is the frequency with which a particular peak is encountered in individual acquisitions within the full series of acquisitions [34] . Normalizing for peak occupancy is often used for enhancing coverage and reproducibility of peak detection.…”

Section: Total Lipid Analyses and De Novo Lipid Identification And Qumentioning

confidence: 99%

Lipidomic mass spectrometry and its application in neuroscience

Enriquez-Algeciras¹,

Bhattacharya²

2013

WJBC

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can be regarded to as mass analyzers. There are those that separate and analyze the product ion fragments in space (spatial) and those which separate product ions in time in the same space (temporal). Databases and standardized instrument parameters have further aided the capabilities of the spatial instruments while recent advances in bioinformatics have made the identification and quantification possible using temporal instruments.© 2013 Baishideng Publishing Group co., Limited. All rights reserved.Key words: Mass spectrometry; Lipidomics; Phospholipids; Serial signaling; Neuroscience Core tip: Mass spectrometry offers a degree of simplicity and sophistication to the biological sciences. In this review we are focusing on its application towards the analysis of lipids in neuroscience. Lipids have a variety of functions, they surround neurons, provide insulation for transmission of signals, an environment for facilitating motility and migration of astrocytes and other cell types, among many other functions. Recent advances in mass spectrometry have enabled quantification of lipids directly extracted from complex biological mixtures in the neuronal system with the help of databases, standardized instrument parameters and bioinformatics. In this review, we intend to highlight all recent efforts with an emphasis on its application to neuroscience.Enriquez-Algeciras M, Bhattacharya SK. Lipidomic mass spectrometry and its application in neuroscience. World J Biol Chem 2013; 4(4): 102-110 Available from:

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A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

Cited by 372 publications

References 44 publications

Stimulation, Inhibition, or Stabilization of Na,K-ATPase Caused by Specific Lipid Interactions at Distinct Sites

Stimulation, Inhibition, or Stabilization of Na,K-ATPase Caused by Specific Lipid Interactions at Distinct Sites

Liver-Restricted Repin1 Deficiency Improves Whole-Body Insulin Sensitivity, Alters Lipid Metabolism, and Causes Secondary Changes in Adipose Tissue in Mice

Lipidomic mass spectrometry and its application in neuroscience

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