Lipid Data Analyzer: The LDA algorithm against the in silico library LipidBlast (LipidBlast benchmarking experiment)

ABSTRACT: 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: MTBLS391 MTBLS394 MTBLS396 MTBLS398 MTBLS462

OTHER RELATED OMICS DATASETS IN: PXD009709

INSTRUMENT(S): Control experiment 1 positive - Orbitrap velos CID (Thermo Scientific), Biological experiment positive - QTRAP 4000 (AB Sciex), Control experiment 1 negative - Orbitrap velos CID (Thermo Scientific), Biological experiment negative - QTRAP 4000 (AB Sciex), Biological experiment negative - Orbitrap velos CID (Thermo Scientific), Biological experiment positive - Orbitrap velos CID (Thermo Scientific)

SUBMITTER: Juergen Hartler 

PROVIDER: MTBLS397 | MetaboLights | 2017-11-07

REPOSITORIES: MetaboLights