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Gerhard G. Thallinger

LC-MS/MS data from complex lipid samples carries the potential to elucidate many structural
features of lipids. It provides information about the fatty acids and in many cases about
their regio-isomeric position. However, the MS/MS spectra of lipids can vary tremendously,
because the fragmentation process depends on parameters like the used mass spectrometer,
fragmentation collision energy, charge state, and adduct ions. Due to this diversity,
a generally applicable bioinformatics tool for the automated analysis of lipidomics LC-MS/MS
experiments is still missing. The few existing tools do either not exploit the advantages
of liquid chromatography or are applicable to specific lipid classes and/or an experimental
setup only. Furthermore, end users cannot customize the software for their specific
fragmentation spectra.

This project's global aim is to develop a versatile and generally applicable method for high
throughput determination of lipid structural fatty acid composition from LC-MS/MS data, easily
adaptable to different mass spectrometers and experimental setups. The general applicability will
be facilitated by a newly developed language for the description of MS/MS fragmentation spectra.
Based on this language, a novel algorithm will identify the lipid and its deducible compositional
features. Furthermore, we want to supply a graphical user interface for the definition of rules
describing the spectra, and supply pre-defined rule-sets for the most common mass spectrometers.

LC MS/MS data analysis delivers in a single experiment the most sensitive information about the
lipidome of a complex biological sample. A successful implementation of a generally applicable tool
for the automated analysis of such data will accelerate lipid analysis enormously. This will give
a more complete picture on the lipidome and its changes which is ideally suited for top down approaches
and investigation of biological questions.