The Experts below are selected from a list of 5133 Experts worldwide ranked by ideXlab platform
Andrej Shevchenko - One of the best experts on this subject based on the ideXlab platform.
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shotgun lipidomics and mass spectrometry imaging unveil diversity and dynamics in gammarus fossarum lipid composition
iScience, 2021Co-Authors: Oskar Knittelfelder, Andrej Shevchenko, Olivier Geffard, Yohann Clement, Eric Testet, Nicolas Elie, David Touboul, Khedidja Abbaci, Jerome Lemoine, Arnaud ChaumotAbstract:Summary Sentinel species are playing an indispensable role in monitoring environmental pollution in aquatic ecosystems. Many pollutants found in water prove to be endocrine disrupting chemicals that could cause disruptions in lipid homeostasis in aquatic species. A comprehensive profiling of the Lipidome of these species is thus an essential step toward understanding the mechanism of toxicity induced by pollutants. Both the composition and spatial distribution of lipids in freshwater crustacean Gammarus fossarum were extensively examined herein. The baseline Lipidome of gammarids of different sex and reproductive stages was established by high throughput shotgun lipidomics. Spatial lipid mapping by high resolution mass spectrometry imaging led to the discovery of sulfate-based lipids in hepatopancreas and their accumulation in mature oocytes. A diverse and dynamic lipid composition in G. fossarum was uncovered, which deepens our understanding of the biochemical changes during development and which could serve as a reference for future ecotoxicological studies.
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shotgun lipidomics and mass spectrometry imaging unveil diversity and dynamics in lipid composition in gammarus fossarum
Social Science Research Network, 2020Co-Authors: Oskar Knittelfelder, Andrej Shevchenko, Olivier Geffard, Yohann Clement, Eric Testet, Nicolas Elie, David Touboul, Khedidja Abbaci, Jerome Lemoine, Arnaud ChaumotAbstract:Sentinel species are playing an indispensable role in monitoring environmental pollution in aquatic ecosystems. Many pollutants found in water prove to be endocrine disrupting chemicals that could cause disruptions in lipid homeostasis in aquatic species. A comprehensive profiling of the Lipidome of these species is thus an essential step towards understanding the mechanism of toxicity induced by pollutants. We here extensively examined both the composition and spatial distribution of lipids in freshwater crustacean Gammarus fossarum. The baseline Lipidome of gammarids of different gender and reproductive stage was established by high throughput shotgun lipidomics. Spatial lipid mapping by high resolution mass spectrometry imaging led to the discovery of sulfate-based lipids in hepatopancreas and their accumulation in mature oocytes. We uncovered in G. fossarum a diverse and dynamic lipid composition that deepens our understanding of the biochemical changes during development and which could serve as a reference for future ecotoxicological studies.
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monitoring membrane Lipidome turnover by metabolic 15n labeling and shotgun ultra high resolution orbitrap fourier transform mass spectrometry
Analytical Chemistry, 2017Co-Authors: Kai Schuhmann, Unal Coskun, Kristina Srzentic, Konstantin O Nagornov, Henrik Thomas, Theresia Gutmann, Yury O Tsybin, Andrej ShevchenkoAbstract:Lipidomes undergo permanent extensive remodeling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic 15N labeling and shotgun ultra-high-resolution mass spectrometry (sUHR) to quantify the absolute (molar) abundance and determine the turnover rate of glycerophospholipids and sphingolipids by direct analysis of total lipid extracts. sUHR performed on a commercial Orbitrap Elite instrument at the mass resolution of 1.35 × 106 (m/z 200) baseline resolved peaks of 13C isotopes of unlabeled and monoisotopic peaks of 15N labeled lipids (Δm = 0.0063 Da). Therefore, the rate of metabolic 15N labeling of individual lipid species could be determined without compromising the scope, accuracy, and dynamic range of full-Lipidome quantitative shotgun profiling. As a proof of concept, we employed sUHR to determine the Lipidome composition and fluxes of 62 nitrogen-containing membrane lipids in human hepatoma HepG2 cells.
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shotgun lipidomics on high resolution mass spectrometers
Cold Spring Harbor Perspectives in Biology, 2011Co-Authors: Dominik Schwudke, Kai Schuhmann, Stefan R Bornstein, Ronny Herzog, Andrej ShevchenkoAbstract:Despite their compositional complexity, Lipidomes comprise a large number of isobaric species that cannot be distinguished by conventional low resolution mass spectrometry and therefore in-depth MS/MS analysis was required for their accurate quantification. Here we argue that the progress in high resolution mass spectrometry is changing the concept of Lipidome characterization. Because exact masses of isobaric species belonging to different lipid classes are not necessarily identical, they can now be distinguished and directly quantified in total lipid extracts. By streamlining and simplifying the molecular characterization of Lipidomes, high resolution mass spectrometry has developed into a generic tool for cell biology and molecular medicine.
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a novel informatics concept for high throughput shotgun lipidomics based on the molecular fragmentation query language
Genome Biology, 2011Co-Authors: Kai Schuhmann, Stefan R Bornstein, Dominik Schwudke, Ronny Herzog, Julio L Sampaio, Michael Schroeder, Andrej ShevchenkoAbstract:Shotgun Lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of Lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.
Christer S Ejsing - One of the best experts on this subject based on the ideXlab platform.
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comprehensive Lipidome analysis by shotgun lipidomics on a hybrid quadrupole orbitrap linear ion trap mass spectrometer
Journal of the American Society for Mass Spectrometry, 2015Co-Authors: Reinaldo Almeida, Elena Sokol, Josch K Pauling, Hans Kristian Hannibalbach, Christer S EjsingAbstract:Here we report on the application of a novel shotgun lipidomics platform featuring an Orbitrap Fusion mass spectrometer equipped with an automated nanoelectrospray ion source. To assess the performance of the platform for in-depth Lipidome analysis, we evaluated various instrument parameters, including its high resolution power unsurpassed by any other contemporary Orbitrap instrumentation, its dynamic quantification range and its efficacy for in-depth structural characterization of molecular lipid species by quadrupole-based higher-energy collisional dissociation (HCD), and ion trap-based resonant-excitation collision-induced dissociation (CID). This evaluation demonstrated that FTMS analysis with a resolution setting of 450,000 allows distinguishing isotopes from different lipid species and features a linear dynamic quantification range of at least four orders of magnitude. Evaluation of fragmentation analysis demonstrated that combined use of HCD and CID yields complementary fragment ions of molecular lipid species. To support global Lipidome analysis, we designed a method, termed MSALL, featuring high resolution FTMS analysis for lipid quantification, and FTMS2 analysis using both HCD and CID and ITMS3 analysis utilizing dual CID for in-depth structural characterization of molecular glycerophospholipid species. The performance of the MSALL method was benchmarked in a comparative analysis of mouse cerebellum and hippocampus. This analysis demonstrated extensive Lipidome quantification covering 311 lipid species encompassing 20 lipid classes, and identification of 202 distinct molecular glycerophospholipid species when applying a novel high confidence filtering strategy. The work presented here validates the performance of the Orbitrap Fusion mass spectrometer for in-depth Lipidome analysis.
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analysis of lipid experiments alex a software framework for analysis of high resolution shotgun lipidomics data
PLOS ONE, 2013Co-Authors: Peter Husen, Kim Ekroos, Kirill Tarasov, Maciej Katafiasz, Elena Sokol, Johannes Vogt, Jan Baumgart, Robert Nitsch, Christer S EjsingAbstract:Global lipidomics analysis across large sample sizes produces high-content datasets that require dedicated software tools supporting lipid identification and quantification, efficient data management and Lipidome visualization. Here we present a novel software-based platform for streamlined data processing, management and visualization of shotgun lipidomics data acquired using high-resolution Orbitrap mass spectrometry. The platform features the ALEX framework designed for automated identification and export of lipid species intensity directly from proprietary mass spectral data files, and an auxiliary workflow using database exploration tools for integration of sample information, computation of lipid abundance and Lipidome visualization. A key feature of the platform is the organization of lipidomics data in ”database table format” which provides the user with an unsurpassed flexibility for rapid Lipidome navigation using selected features within the dataset. To demonstrate the efficacy of the platform, we present a comparative neurolipidomics study of cerebellum, hippocampus and somatosensory barrel cortex (S1BF) from wild-type and knockout mice devoid of the putative lipid phosphate phosphatase PRG-1 (plasticity related gene-1). The presented framework is generic, extendable to processing and integration of other lipidomic data structures, can be interfaced with post-processing protocols supporting statistical testing and multivariate analysis, and can serve as an avenue for disseminating lipidomics data within the scientific community. The ALEX software is available at www.msLipidomics.info.
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Membrane Lipidome of an epithelial cell line
Proceedings of the National Academy of Sciences, 2011Co-Authors: Julio L Sampaio, Mathias J. Gerl, Christian Klose, Keith Simons, Christer S Ejsing, Andrej ShevchenkoAbstract:Tissue differentiation is an important process that involves major cellular membrane remodeling. We used Madin-Darby canine kidney cells as a model for epithelium formation and investigated the remodeling of the total cell membrane Lipidome during the transition from a nonpolarized morphology to an epithelial morphology and vice versa. To achieve this, we developed a shotgun-based lipidomics workflow that enabled the absolute quantification of mammalian membrane Lipidomes with minimal sample processing from low sample amounts. Epithelial morphogenesis was accompanied by a major shift from sphingomyelin to glycosphingolipid, together with an increase in plasmalogen, phosphatidylethanolamine, and cholesterol content, whereas the opposite changes took place during an epithelial-to-mesenchymal transition. Moreover, during polarization, the sphingolipids became longer, more saturated, and more hydroxylated as required to generate an apical membrane domain that serves as a protective barrier for the epithelial sheet.
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global analysis of the yeast Lipidome by quantitative shotgun mass spectrometry
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Christer S Ejsing, Julio L Sampaio, Kim Ekroos, Kai Simons, Vineeth Surendranath, Eva Duchoslav, Robin W Klemm, Andrej ShevchenkoAbstract:Although the transcriptome, proteome, and interactome of several eukaryotic model organisms have been described in detail, Lipidomes remain relatively uncharacterized. Using Saccharomyces cerevisiae as an example, we demonstrate that automated shotgun lipidomics analysis enabled Lipidome-wide absolute quantification of individual molecular lipid species by streamlined processing of a single sample of only 2 million yeast cells. By comparative lipidomics, we achieved the absolute quantification of 250 molecular lipid species covering 21 major lipid classes. This analysis provided ≈95% coverage of the yeast Lipidome achieved with 125-fold improvement in sensitivity compared with previous approaches. Comparative lipidomics demonstrated that growth temperature and defects in lipid biosynthesis induce ripple effects throughout the molecular composition of the yeast Lipidome. This work serves as a resource for molecular characterization of eukaryotic Lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches.
Ronny Herzog - One of the best experts on this subject based on the ideXlab platform.
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large scale human skin lipidomics by quantitative high throughput shotgun mass spectrometry
Scientific Reports, 2017Co-Authors: Tomasz Sadowski, Mathias J. Gerl, Christian Klose, Ronny Herzog, Kai Simons, Anna Wojcikmaciejewicz, Adam Reich, Michal A SurmaAbstract:The lipid composition of human skin is essential for its function; however the simultaneous quantification of a wide range of stratum corneum (SC) and sebaceous lipids is not trivial. We developed and validated a quantitative high-throughput shotgun mass spectrometry-based platform for lipid analysis of tape-stripped SC skin samples. It features coverage of 16 lipid classes; total quantification to the level of individual lipid molecules; high reproducibility and high-throughput capabilities. With this method we conducted a large lipidomic survey of 268 human SC samples, where we investigated the relationship between sampling depth and lipid composition, Lipidome variability in samples from 14 different sampling sites on the human body and finally, we assessed the impact of age and sex on Lipidome variability in 104 healthy subjects. We found sebaceous lipids to constitute an abundant component of the SC Lipidome as they diffuse into the topmost SC layers forming a gradient. Lipidomic variability with respect to sampling depth, site and subject is considerable, and mainly accredited to sebaceous lipids, while stratum corneum lipids vary less. This stresses the importance of sampling design and the role of sebaceous lipids in skin studies.
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shotgun lipidomics on high resolution mass spectrometers
Cold Spring Harbor Perspectives in Biology, 2011Co-Authors: Dominik Schwudke, Kai Schuhmann, Stefan R Bornstein, Ronny Herzog, Andrej ShevchenkoAbstract:Despite their compositional complexity, Lipidomes comprise a large number of isobaric species that cannot be distinguished by conventional low resolution mass spectrometry and therefore in-depth MS/MS analysis was required for their accurate quantification. Here we argue that the progress in high resolution mass spectrometry is changing the concept of Lipidome characterization. Because exact masses of isobaric species belonging to different lipid classes are not necessarily identical, they can now be distinguished and directly quantified in total lipid extracts. By streamlining and simplifying the molecular characterization of Lipidomes, high resolution mass spectrometry has developed into a generic tool for cell biology and molecular medicine.
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a novel informatics concept for high throughput shotgun lipidomics based on the molecular fragmentation query language
Genome Biology, 2011Co-Authors: Kai Schuhmann, Stefan R Bornstein, Dominik Schwudke, Ronny Herzog, Julio L Sampaio, Michael Schroeder, Andrej ShevchenkoAbstract:Shotgun Lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of Lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.
Dominik Schwudke - One of the best experts on this subject based on the ideXlab platform.
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Lipidomes of lung cancer and tumour-free lung tissues reveal distinct molecular signatures for cancer differentiation, age, inflammation, and pulmonary emphysema
Nature Publishing Group, 2017Co-Authors: Lars F. Eggers, Julia Müller, Chakravarthy Marella, Verena Scholz, Henrik Watz, Christian Kugler, Klaus F. Rabe, Torsten Goldmann, Dominik SchwudkeAbstract:Abstract Little is known about the human lung Lipidome, its variability in different physiological states, its alterations during carcinogenesis and the development of pulmonary emphysema. We investigated how health status might be mirrored in the lung Lipidome. Tissues were sampled for both lipidomic and histological analysis. Using a screening approach, we characterised Lipidomes of lung cancer tissues and corresponding tumour-free alveolar tissues. We quantified 311 lipids from 11 classes in 43 tissue samples from 26 patients. Tumour tissues exhibited elevated levels of triacylglycerols and cholesteryl esters, as well as a significantly lower abundance of phosphatidylglycerols, which are typical lung surfactant components. Adenocarcinomas and squamous cell carcinomas were distinguished with high specificity based on lipid panels. Lipidomes of tumour biopsy samples showed clear changes depending on their histology and, in particular, their proportion of active tumour cells and stroma. Partial least squares regression showed correlations between lipid profiles of tumour-free alveolar tissues and the degree of emphysema, inflammation status, and the age of patients. Unsaturated long-chain phosphatidylserines and phosphatidylinositols showed a positive correlation with a worsened emphysema status and ageing. This work provides a resource for the human lung Lipidome and a systematic data analysis strategy to link clinical characteristics and histology
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shotgun lipidomics on high resolution mass spectrometers
Cold Spring Harbor Perspectives in Biology, 2011Co-Authors: Dominik Schwudke, Kai Schuhmann, Stefan R Bornstein, Ronny Herzog, Andrej ShevchenkoAbstract:Despite their compositional complexity, Lipidomes comprise a large number of isobaric species that cannot be distinguished by conventional low resolution mass spectrometry and therefore in-depth MS/MS analysis was required for their accurate quantification. Here we argue that the progress in high resolution mass spectrometry is changing the concept of Lipidome characterization. Because exact masses of isobaric species belonging to different lipid classes are not necessarily identical, they can now be distinguished and directly quantified in total lipid extracts. By streamlining and simplifying the molecular characterization of Lipidomes, high resolution mass spectrometry has developed into a generic tool for cell biology and molecular medicine.
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a novel informatics concept for high throughput shotgun lipidomics based on the molecular fragmentation query language
Genome Biology, 2011Co-Authors: Kai Schuhmann, Stefan R Bornstein, Dominik Schwudke, Ronny Herzog, Julio L Sampaio, Michael Schroeder, Andrej ShevchenkoAbstract:Shotgun Lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of Lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.
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top down lipidomics reveals ether lipid deficiency in blood plasma of hypertensive patients
PLOS ONE, 2009Co-Authors: Juerge Graessle, Dominik Schwudke, Pete Schwarz, Andrej Shevchenko, Stefa R OrnsteiAbstract:Background: Dyslipoproteinemia, obesity and insulin resistance are integrative constituents of the metabolic syndrome and are major risk factors for hypertension. The objective of this study was to determine whether hypertension specifically affects the plasma Lipidome independently and differently from the effects induced by obesity and insulin resistance. Methodology/Principal Findings: We screened the plasma Lipidome of 19 men with hypertension and 51 normotensive male controls by top-down shotgun profiling on a LTQ Orbitrap hybrid mass spectrometer. The analysis encompassed 95 lipid species of 10 major lipid classes. Obesity resulted in generally higher lipid load in blood plasma, while the content of tri- and diacylglycerols increased dramatically. Insulin resistance, defined by HOMA-IR .3.5 and controlled for BMI, had little effect on the plasma Lipidome. Importantly, we observed that in blood plasma of hypertensive individuals the overall content of ether lipids decreased. Ether phosphatidylcholines and ether phosphatidylethanolamines, that comprise arachidonic (20:4) and docosapentaenoic (22:5) fatty acid moieties, were specifically diminished. The content of free cholesterol also decreased, although conventional clinical lipid homeostasis indices remained unaffected. Conclusions/Significance: Top-down shotgun lipidomics demonstrated that hypertension is accompanied by specific reduction of the content of ether lipids and free cholesterol that occurred independently of lipidomic alterations induced by obesity and insulin resistance. These results may form the basis for novel preventive and dietary strategies alleviating the severity of hypertension.
Kai Simons - One of the best experts on this subject based on the ideXlab platform.
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comprehensive and quantitative analysis of white and brown adipose tissue by shotgun lipidomics
bioRxiv, 2018Co-Authors: Michal Grzybek, Christian Klose, Michal A Surma, Alessandra Palladini, Vasileia Ismini Alexaki, Kai Simons, Triantafyllos Chavakis, Unal CoskunAbstract:Shotgun lipidomics enables an extensive analysis of lipids from tissues and fluids. Each specimen requires appropriate extraction and processing procedures to ensure good coverage and reproducible quantification of the Lipidome. Adipose tissue (AT) has become a research focus with regard to its involvement in obesity-related pathologies. However, the quantification of the AT Lipidome is particularly challenging due to the predominance of triacylglycerides, which elicit high ion suppression of the remaining lipid classes. We present a new and validated method for shotgun lipidomics of AT, which tailors the lipid extraction procedure to the target specimen and features high reproducibility with a linear dynamic range of at least 4 orders of magnitude for all lipid classes. Utilizing this method, we observed tissue-specific and diet-related differences in three AT types (brown, gonadal, inguinal subcutaneous) from lean and obese mice. Brown AT exhibited a distinct lipidomic profile with the greatest lipid class diversity and responded to high-fat diet by altering its lipid composition, which shifted towards that of white AT. Moreover, diet-induced obesity promoted an overall remodelling of the Lipidome, where all three AT types featured a significant increase in longer and more unsaturated triacylglyceride and phospholipid species. The here presented method facilitates reproducible systematic lipidomic profiling of AT and could be integrated with further -omics approaches used in (pre-)clinical research, in order to advance the understanding of the molecular metabolic dynamics involved in the pathogenesis of obesity-associated disorders.
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large scale human skin lipidomics by quantitative high throughput shotgun mass spectrometry
Scientific Reports, 2017Co-Authors: Tomasz Sadowski, Mathias J. Gerl, Christian Klose, Ronny Herzog, Kai Simons, Anna Wojcikmaciejewicz, Adam Reich, Michal A SurmaAbstract:The lipid composition of human skin is essential for its function; however the simultaneous quantification of a wide range of stratum corneum (SC) and sebaceous lipids is not trivial. We developed and validated a quantitative high-throughput shotgun mass spectrometry-based platform for lipid analysis of tape-stripped SC skin samples. It features coverage of 16 lipid classes; total quantification to the level of individual lipid molecules; high reproducibility and high-throughput capabilities. With this method we conducted a large lipidomic survey of 268 human SC samples, where we investigated the relationship between sampling depth and lipid composition, Lipidome variability in samples from 14 different sampling sites on the human body and finally, we assessed the impact of age and sex on Lipidome variability in 104 healthy subjects. We found sebaceous lipids to constitute an abundant component of the SC Lipidome as they diffuse into the topmost SC layers forming a gradient. Lipidomic variability with respect to sampling depth, site and subject is considerable, and mainly accredited to sebaceous lipids, while stratum corneum lipids vary less. This stresses the importance of sampling design and the role of sebaceous lipids in skin studies.
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lipidomics coming to grips with lipid diversity
Nature Reviews Molecular Cell Biology, 2010Co-Authors: Andrej Shevchenko, Kai SimonsAbstract:Although lipids are biomolecules with seemingly simple chemical structures, the molecular composition of the cellular Lipidome is complex and, currently, poorly understood. The exact mechanisms of how compositional complexity affects cell homeostasis and its regulation also remain unclear. This emerging field is developing sensitive mass spectrometry technologies for the quantitative characterization of the Lipidome. Here, we argue that lipidomics will become an essential tool kit in cell and developmental biology, molecular medicine and nutrition.
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global analysis of the yeast Lipidome by quantitative shotgun mass spectrometry
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Christer S Ejsing, Julio L Sampaio, Kim Ekroos, Kai Simons, Vineeth Surendranath, Eva Duchoslav, Robin W Klemm, Andrej ShevchenkoAbstract:Although the transcriptome, proteome, and interactome of several eukaryotic model organisms have been described in detail, Lipidomes remain relatively uncharacterized. Using Saccharomyces cerevisiae as an example, we demonstrate that automated shotgun lipidomics analysis enabled Lipidome-wide absolute quantification of individual molecular lipid species by streamlined processing of a single sample of only 2 million yeast cells. By comparative lipidomics, we achieved the absolute quantification of 250 molecular lipid species covering 21 major lipid classes. This analysis provided ≈95% coverage of the yeast Lipidome achieved with 125-fold improvement in sensitivity compared with previous approaches. Comparative lipidomics demonstrated that growth temperature and defects in lipid biosynthesis induce ripple effects throughout the molecular composition of the yeast Lipidome. This work serves as a resource for molecular characterization of eukaryotic Lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches.