Marine metabolomics: measurement of metabolites in seawater by gas chromatography mass spectrometry (Method development)
Ontology highlight
ABSTRACT:
Method development is reported in the current study MTBLS826.
The effect of salt and water on metabolite detection is reported in MTBLS839.
Cell culture sampling is reported in MTBLS843.
Environmental sampling is reported in MTBLS844.
Method quantification is reported in MTBLS848.
Solid phase extraction is reported in MTBLS849.
Linked Studies: MTBLS839 MTBLS843 MTBLS844 MTBLS848 MTBLS849
INSTRUMENT(S): Gas Chromatography MS - Positive (GC-MS (Positive))
SUBMITTER: Manuel Liebeke
PROVIDER: MTBLS826 | MetaboLights | 2019-11-15
REPOSITORIES: MetaboLights
Similar Datasets
Project description:One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats. </br></br> Method quantification is reported in the current study MTBLS848.</br> Method development is reported in MTBLS826.</br> The effect of salt and water on metabolite detection is reported in MTBLS839.</br> Cell culture sampling is reported in MTBLS843.</br> Environmental sampling is reported in MTBLS844.</br> Solid phase extraction is reported in MTBLS849.</br> </br><br/> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS826' target='_blank'><span class='label label-success'>MTBLS826</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS839' target='_blank'><span class='label label-success'>MTBLS839</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS843' target='_blank'><span class='label label-success'>MTBLS843</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS844' target='_blank'><span class='label label-success'>MTBLS844</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS849' target='_blank'><span class='label label-success'>MTBLS849</span></a>
2019-11-15 | MTBLS848 | MetaboLights
Project description:One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats. </br></br> Solid phase extraction is reported in the current study MTBLS849.</br> Method development is reported in MTBLS826.</br> The effect of salt and water on metabolite detection is reported in MTBLS839.</br> Cell culture sampling is reported in MTBLS843.</br> Environmental sampling is reported in MTBLS844.</br> Method quantification is reported in MTBLS848.</br> </br><br/> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS826' target='_blank'><span class='label label-success'>MTBLS826</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS839' target='_blank'><span class='label label-success'>MTBLS839</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS843' target='_blank'><span class='label label-success'>MTBLS843</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS844' target='_blank'><span class='label label-success'>MTBLS844</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS848' target='_blank'><span class='label label-success'>MTBLS848</span></a>
2019-11-15 | MTBLS849 | MetaboLights
Project description:One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats. </br></br> The effect of salt and water on metabolite detection is reported in the current study MTBLS839.</br> Method development is reported in MTBLS826.</br> Cell culture sampling is reported MTBLS843.</br> Environmental sampling is reported MTBLS844.</br> Method quantification is reported in MTBLS848.</br> Solid phase extraction is reported in MTBLS849.</br> </br><br/> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS826' target='_blank'><span class='label label-success'>MTBLS826</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS843' target='_blank'><span class='label label-success'>MTBLS843</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS844' target='_blank'><span class='label label-success'>MTBLS844</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS848' target='_blank'><span class='label label-success'>MTBLS848</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS849' target='_blank'><span class='label label-success'>MTBLS849</span></a>
2019-11-15 | MTBLS839 | MetaboLights
Project description:<p>One of the major bottlenecks in describing marine ecosystems is characterizing the metabolome of seawater, as salt prevents metabolite analysis. We present SeaMet, a method that can detect hundreds of metabolites in less than one ml of seawater and quantifies them down to nano-molar levels using gas chromatography-mass spectrometry. Our method provides a major advance in marine metabolomics by enabling the unbiased analysis of primary metabolites across saltwater habitats. </p><p><br></p><p>Cell culture sampling is reported in the current study.</p><p>Method development is reported in <a href="https://www.ebi.ac.uk/metabolights/MTBLS826" target="_blank">MTBLS826</a></p><p>The effect of salt and water on metabolite detection is reported in <a href="https://www.ebi.ac.uk/metabolights/MTBLS839" target="_blank">MTBLS839</a></p><p>Environmental sampling is reported in <a href="https://www.ebi.ac.uk/metabolights/MTBLS844" target="_blank">MTBLS844</a></p><p>Method quantification is reported in <a href="https://www.ebi.ac.uk/metabolights/MTBLS848" target="_blank">MTBLS848</a></p><p>Solid phase extraction is reported in <a href="https://www.ebi.ac.uk/metabolights/MTBLS849" target="_blank">MTBLS849</a></p>
2019-11-15 | MTBLS843 | MetaboLights
Project description:Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2) provides automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using embedded rule sets. Using various low- and high-resolution mass spectrometry instruments with several collision energies, the method's platform independence is proved. The software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete. </br></br> LDA identified several novel lipid molecular species and novel regio-isomeric species; we consider a lipid species as “novel” if it is neither present in LIPID MAPS Structure Database, ChEBI, CyberLipid, HMDB, nor YMDB. Where evidence relies on fragments of very small intensity, high resolution HCD mode was used for final characterization. These data are presented here (CID mode data can be found in MTBLS397 - both biological experiments for Orbitrap Velos CID). Moreover, we present in this study data showing the LDA's ability to distinguish regio-isomeric standards under certain chromatographic conditions. </br></br> Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394.</br> Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391.</br>Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398.</br>Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396.</br>LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397.</br><br/>Linked Studies:<a href='https://www.ebi.ac.uk/metabolights/MTBLS391' target='_blank'><span class='label label-success'>MTBLS391</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS394' target='_blank'><span class='label label-success'>MTBLS394</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'><span class='label label-success'>MTBLS396</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS397' target='_blank'><span class='label label-success'>MTBLS397</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' target='_blank'><span class='label label-success'>MTBLS398</span></a>
2020-08-01 | MSV000085878 | GNPS
Project description:The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyse the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signalling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry. </br></br> The GC-MS assay is reported in the current study MTBLS634. </br> The General LC-MS assay is reported in MTBLS629. </br> The Lipidomic LC-MS assay is reported in MTBLS631. </br></br> The CE-MS assay is reported in MTBLS633. </br></br> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS629' target='_blank'><span class='label label-success'>MTBLS629</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS631' target='_blank'><span class='label label-success'>MTBLS631</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS633' target='_blank'><span class='label label-success'>MTBLS633</span></a>
2018-11-06 | MTBLS634 | MetaboLights
Project description:The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyse the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signalling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry. </br></br> The General LC-MS assay is reported in the current study MTBLS629. </br> The Lipidomic LC-MS assay is reported in MTBLS631. </br> The CE-MS assay is reported in MTBLS633. </br> The GC-MS assay is reported in MTBLS634. </br></br> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS631' target='_blank'><span class='label label-success'>MTBLS631</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS633' target='_blank'><span class='label label-success'>MTBLS633</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS634' target='_blank'><span class='label label-success'>MTBLS634</span></a>
2018-11-06 | MTBLS629 | MetaboLights
Project description:The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyse the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signalling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry. </br></br> The CE-MS assay is reported in the current study MTBLS633. </br> The General LC-MS assay is reported in MTBLS629. </br> The Lipidomic LC-MS assay is reported in MTBLS631. </br> The GC-MS assay is reported in MTBLS634. </br></br> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS629' target='_blank'><span class='label label-success'>MTBLS629</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS631' target='_blank'><span class='label label-success'>MTBLS631</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS634' target='_blank'><span class='label label-success'>MTBLS634</span></a>
2018-11-06 | MTBLS633 | MetaboLights
Project description:The characterization of specialized cell subpopulations in a heterogeneous tissue is essential for understanding organ function in health and disease. A popular method of cell isolation is fluorescence-activated cell sorting (FACS) based on probes that bind surface or intracellular markers. In this study, we analyse the impact of FACS on the cell metabolome of mouse peritoneal macrophages. Compared with directly pelleted macrophages, FACS-treated cells had an altered content of metabolites related to the plasma membrane, activating a mechanosensory signalling cascade causing inflammation-like stress. The procedure also triggered alterations related to energy consumption and cell damage. The observed changes mostly derive from the physical impact on cells during their passage through the instrument. These findings provide evidence of FACS-induced biochemical changes, which should be taken into account in the design of robust metabolic assays of cells separated by flow cytometry. </br></br> The Lipidomic LC-MS assay is reported in the current study MTBLS631. </br> The General LC-MS assay is reported in MTBLS629. </br> The CE-MS assay is reported in MTBLS633. </br> The GC-MS assay is reported in MTBLS634. </br></br> Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS629' target='_blank'><span class='label label-success'>MTBLS629</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS633' target='_blank'><span class='label label-success'>MTBLS633</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS634' target='_blank'><span class='label label-success'>MTBLS634</span></a>
2018-11-06 | MTBLS631 | MetaboLights
Project description:Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2) provides automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using embedded rule sets. Using various low- and high-resolution mass spectrometry instruments with several collision energies, the method's platform independence is proved. The software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete. </br></br> The basic fragment rules are based on published results. From the experimental data, the rules were adapted and extended by visual inspection of spectra. Detectable fragments, mandatory fragment derived intensity rules, and extracted decisive differences for many isobaric subclasses/adducts were all identified. In addition, intensity relationships characteristic for sn-position assignment were determined. </br></br> Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391.</br> Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398.</br> Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396.</br> LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397.</br> HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462.</br> <br/>Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS391' target='_blank'><span class='label label-success'>MTBLS391</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'><span class='label label-success'>MTBLS396</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS397' target='_blank'><span class='label label-success'>MTBLS397</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' target='_blank'><span class='label label-success'>MTBLS398</span></a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS462' target='_blank'><span class='label label-success'>MTBLS462</span></a>
2017-10-27 | MTBLS394 | MetaboLights