Lipid Species Annotation at Double Bond Position Level with Custom Databases by Extension of the MZmine 2 Open-Source Software Package

In recent years, proprietary and open-source bioinformatics software tools have been developed for the identification of lipids in complex biological samples based on high-resolution mass spectrometry data. These existent software tools often rely on publicly available lipid databases, such as LIPID MAPS, which, in some cases, only contain a limited number of lipid species for a specific lipid class. Other software solutions implement their own lipid species databases, which are often confined regarding implemented lipid classes, such as phospholipids. To address these drawbacks, we provide an extension of the widely used open-source metabolomics software MZmine 2, which enables the annotation of detected chromatographic features as lipid species. The extension is designed for straightforward generation of a custom database for selected lipid classes. Furthermore, each lipid’s sum formula of the created database can be rapidly modified to search for derivatization products, oxidation products, in-source fragments, or adducts. The versatility will be exemplified by a liquid chromatography–high resolution mass spectrometry data set with postcolumn Paternò–Büchi derivatization. The derivatization reaction was performed to pinpoint the double bond positions in diacylglyceryltrimethylhomoserine lipid species in a lipid extract of a green algae (Chlamydomonas reinhardtii) sample. The developed Lipid Search module extension of MZmine 2 supports the identification of lipids as far as double bond position level