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Novel strategies for targeted lipidomics in complex biological systems
Lipids are fundamental biomolecules deeply involved in numerous biological processes. To elucidate the roles of lipids in biological systems, the study of lipidomics emerged with support from state-of-the-art analytical techniques. However, the high complexity of lipids resulted in many analytical challenges to obtain analyses of whole lipidomes. Therefore, a strategy called targeted lipidomics focuses on scanning and quantifying of selected groups of lipids only. However, one of the main challenges of targeted lipidomics is the lack of suitable bioinformatics tools and workflows to set up a targeted assay for the huge variety of lipid classes. Thus, the aim of this thesis is to improve the targeted lipidomics workflows, including the creation of targeted assays and the parameters for chromatographic separation, and apply and validate developed workflows to different model systems such as the RAW 264.7 cell line (a community model) or platelets as an ex-vivo model. Firstly, an interim strategy was developed to adapt Skyline (a targeted proteomics software package) for targeted lipidomics analyses. Secondly, LipidCreator was developed, the first open source software fully supporting the targeted lipidomics assay development. LipidCreator not only delivers the computation of fragment masses of over 60 lipid classes, it also provides the functionality to define fragments, introduces stable isotope labeling of lipids for targeted assays, provides an optimization module for collision energy and generates in-silico spectral libraries. This software can either be used as a standalone tool or with Skyline. On the basis of LipidCreator, the high performance chromatography/mass spectrometry-based targeted lipidomics workflows including extraction optimization, lipid category tailored gradients and fragmentation rules in mass spectrometry were established, leading to significantly increased accuracy for the analysis of targeted lipids. Finally, the established targeted approaches were utilized in conjunction with shotgun ...
Novel strategies for targeted lipidomics in complex biological systems
Lipids are fundamental biomolecules deeply involved in numerous biological processes. To elucidate the roles of lipids in biological systems, the study of lipidomics emerged with support from state-of-the-art analytical techniques. However, the high complexity of lipids resulted in many analytical challenges to obtain analyses of whole lipidomes. Therefore, a strategy called targeted lipidomics focuses on scanning and quantifying of selected groups of lipids only. However, one of the main challenges of targeted lipidomics is the lack of suitable bioinformatics tools and workflows to set up a targeted assay for the huge variety of lipid classes. Thus, the aim of this thesis is to improve the targeted lipidomics workflows, including the creation of targeted assays and the parameters for chromatographic separation, and apply and validate developed workflows to different model systems such as the RAW 264.7 cell line (a community model) or platelets as an ex-vivo model. Firstly, an interim strategy was developed to adapt Skyline (a targeted proteomics software package) for targeted lipidomics analyses. Secondly, LipidCreator was developed, the first open source software fully supporting the targeted lipidomics assay development. LipidCreator not only delivers the computation of fragment masses of over 60 lipid classes, it also provides the functionality to define fragments, introduces stable isotope labeling of lipids for targeted assays, provides an optimization module for collision energy and generates in-silico spectral libraries. This software can either be used as a standalone tool or with Skyline. On the basis of LipidCreator, the high performance chromatography/mass spectrometry-based targeted lipidomics workflows including extraction optimization, lipid category tailored gradients and fragmentation rules in mass spectrometry were established, leading to significantly increased accuracy for the analysis of targeted lipids. Finally, the established targeted approaches were utilized in conjunction with shotgun ...
Novel strategies for targeted lipidomics in complex biological systems
Peng, Bing (Autor:in) / Schmitz, Oliver
17.11.2020
Hochschulschrift
Elektronische Ressource
Englisch