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. 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. Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391.Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398.Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396.LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397. Linked Studies:<a href='https://www.ebi.ac.uk/metabolights/MTBLS391' target='_blank'>MTBLS391</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS394' target='_blank'>MTBLS394</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'>MTBLS396</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS397' target='_blank'>MTBLS397</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' target='_blank'>MTBLS398</a>

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. In lipidomics LC-MS/MS experiments, structural isomers within one MS1 peak frequently occur. In this experiment, structural isomeric pairs from PC, PE, PG, PS and TG are mixed in one sample at various concentrations. The algorithm appropriately assigning the respective structural isomers is demonstrated. Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391. Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396. LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397. HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462. Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS391' target='_blank'>MTBLS391</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS394' target='_blank'>MTBLS394</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'>MTBLS396</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS397' target='_blank'>MTBLS397</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS462' target='_blank'>MTBLS462</a>

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. In lipidomics, overlaps of species from isobars from other subclasses/adducts frequently occur. In this experiment, isobars from PC and PE, and from LPC and LPE are mixed in one sample. The LC-method was made worse, so that these species generated overlapping peaks. In this experiment, the LDA's propensity to detect and seperate such species was tested. Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398. Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396. LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397. HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462. Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS394' target='_blank'>MTBLS394</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'>MTBLS396</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS397' target='_blank'>MTBLS397</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' target='_blank'>MTBLS398</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS462' target='_blank'>MTBLS462</a>

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. 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. Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391.Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398.Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396.LipidBlast benchmarking assays for this study can be found in the MetaboLights study MTBLS397. Linked Studies:<a href='https://www.ebi.ac.uk/metabolights/MTBLS391' target='_blank'>MTBLS391</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS394' target='_blank'>MTBLS394</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'>MTBLS396</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS397' target='_blank'>MTBLS397</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' target='_blank'>MTBLS398</a>

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. In a benchmark test of LDA versus LipidBlast, data from both the first control experiment and the biological experiment, both acquired on the Orbitrap Velos Pro in CID +50 and -50, was used. In addition, the biological experiment was benchmarked for the lower resolution QTRAP 4000 for +45 eV and -45 eV. For LipidBlast evaluation, the parameters recommended by NIST MSPepSearchGUI (http://peptide.nist.gov/software/ms_pep_search_gui/MSPepSearch.html) were used. The same m/z tolerances were applied in both LipidBlast and LDA. The specificity and sensitivity of LipidBlast depend on a so called matching factor, a value ranging from 0-999. Using the default setting of 450 for the matching factor, many lipid standards in Control experiment 1 were not detected. Consequently, the matching factor was lowered to 10, in which case LipidBlast detected almost all of the lipid standards in negative ion mode. Further reduction did not improve the sensitivity of LipidBlast. In positive ion mode, irrespective of the matching factor setting, LipidBlast was not able to identify as many lipid molecular species as was LDA. In this benchmark test, only lipid subclasses/adducts that both LDA and LipidBlast are able to detect were used. Correct assignment of lipid species and lipid molecular species identified in liver lipidomes was verified by manual inspection of the spectra, and by aligning them with the respective retention time data.Control experiment 1 assays for this study can be found in the MetaboLights study MTBLS394. Control experiment 2 assays for this study can be found in the MetaboLights study MTBLS391. Control experiment 3 assays for this study can be found in the MetaboLights study MTBLS398. Murine liver lipidome experiment assays for this study can be found in the MetaboLights study MTBLS396. HCD characterization and regioisomer detection assays for this study can be found in the MetaboLights study MTBLS462. Linked Studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS391' target='_blank'>MTBLS391</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS394' target='_blank'>MTBLS394</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' target='_blank'>MTBLS396</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' target='_blank'>MTBLS398</a> <a href='https://www.ebi.ac.uk/metabolights/MTBLS462' target='_blank'>MTBLS462</a>

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. 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. Control experiment 1 assays can be found in the current study MTBLS394.Control experiment 2 assays can be found in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS391' rel='noopener noreferrer' target='_blank'>MTBLS391</a>.Control experiment 3 assays can be found in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS398' rel='noopener noreferrer' target='_blank'>MTBLS398</a>.Murine liver lipidome experiment assays can be found in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS396' rel='noopener noreferrer' target='_blank'>MTBLS396</a>.LipidBlast benchmarking assays can be found in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS397' rel='noopener noreferrer' target='_blank'>MTBLS397</a>.HCD characterization and regioisomer detection assays can be found in study <a href='https://www.ebi.ac.uk/metabolights/MTBLS462' rel='noopener noreferrer' target='_blank'>MTBLS462</a>.

			Action	DRS
	MTBLS396	Other
	FILES	Other
	a_MTBLS396_biol_OrbCID_N_mass_spectrometry.txt	Txt
	a_MTBLS396_biol_OrbCID_P_mass_spectrometry.txt	Txt
	a_MTBLS396_biol_OrbElite_N_mass_spectrometry.txt	Txt

Dataset Information

Lipid Data Analyzer: Analysis of a complex biological system from murine liver samples (Murine liver lipidome experiment)

Dataset's files

Publications

Deciphering lipid structures based on platform-independent decision rules.

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