title: LipidFrag: Improving reliability of in silico fragmentation of lipids and application to the Caenorhabditis elegans lipidome.
abstract: Lipid identification is a major bottleneck in high-throughput lipidomics studies. However, tools for the analysis of lipid tandem MS spectra are rather limited. While the comparison against spectra in reference libraries is one of the preferred methods, these libraries are far from being complete. In order to improve identification rates, the in silico fragmentation tool MetFrag was combined with Lipid Maps and lipid-class specific classifiers which calculate probabilities for lipid class assignments. The resulting LipidFrag workflow was trained and evaluated on different commercially available lipid standard materials, measured with data dependent UPLC-Q-ToF-MS/MS acquisition. The automatic analysis was compared against manual MS/MS spectra interpretation. With the lipid class specific models, identification of the true positives was improved especially for cases where candidate lipids from different lipid classes had similar MetFrag scores by removing up to 56% of false positive results. This LipidFrag approach was then applied to MS/MS spectra of lipid extracts of the nematode Caenorhabditis elegans. Fragments explained by LipidFrag match known fragmentation pathways, e.g., neutral losses of lipid headgroups and fatty acid side chain fragments. Based on prediction models trained on standard lipid materials, high probabilities for correct annotations were achieved, which makes LipidFrag a good choice for automated lipid data analysis and reliability testing of lipid identifications.
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse, Neuherberg, Germany.|Chair of Analytical Food Chemistry, Technische Universität München, Alte Akademie 10, D-85354 Freising-Weihenstephan, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Witting
authors.affiliation: Leibniz Institute of Plant Biochemistry, IPB Halle, Department of Stress and Developmental Biology, Weinberg, Halle, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Ruttkies
authors.affiliation: Leibniz Institute of Plant Biochemistry, IPB Halle, Department of Stress and Developmental Biology, Weinberg, Halle, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Neumann
authors.affiliation: Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse, Neuherberg, Germany.|Chair of Analytical Food Chemistry, Technische Universität München, Alte Akademie 10, D-85354 Freising-Weihenstephan, Germany.
authors.forename: Philippe
authors.initials: P
authors.lastname: Schmitt-Kopplin
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000254:growth & development / Q000378:metabolism*; D003198:Computer Simulation; D008055:Lipids / Q000032:analysis* / Q000737:chemistry*; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D008055:Lipids