Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms

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Abstract

A major challenge for mass spectrometric-based lipidomics, aiming at describing all lipid species in a biological sample, lies in the computational and bioinformatic processing of the large amount of data that arises after data acquisition. Lipid-Pro is a software tool that supports the identification of lipids by interpreting large datasets generated by liquid chromatography - tandem mass spectrometry (LC-MS/MS) using the advanced data-independent acquisition mode MSE. In the MSE mode, the instrument fragments all molecular ions generated from a sample and records time-resolved molecular ion data as well as fragment ion data for every detectable molecular ion. Lipid-Pro matches the retention time-aligned mass-to-charge ratio data of molecular- and fragment ions with a lipid database and generates a report on all identified lipid species. For generation of the lipid database, Lipid-Pro provides a module for construction of lipid species and their fragments using a flexible building block approach. Hence, Lipid-Pro is an easy to use analysis tool to interpret complex MSE lipidomics data and also offers a module to generate a user-specific lipid database.

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Ahmed, Z., Mayr, M., Zeeshan, S., Dandekar, T., Mueller, M. J., & Fekete, A. (2015). Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinformatics, 31(7), 1150–1153. https://doi.org/10.1093/bioinformatics/btu796

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