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

Abstract

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 Paterno−Buchi 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.

Deep-lipidotyping by mass spectrometry: recent technical advances and applications

“…To push detailed structural analysis to the lipids of lower abundances, such as lipid mediators or single-cell lipidome, integration with pre-enrichment methods will help in this regard. With the new capabilities of deep-lipidotyping, of equal importance is development of tools for data analysis and automated lipid annotation at deeper structural levels ( 123 ). This development is critical to speeding up the transfer of new MS methods from expert labs to ordinary lipid analysis labs.…”

Double bond localization in unsaturated rhamnolipid precursors 3-(3-hydroxyalkanoyloxy)alkanoic acids by liquid chromatography–mass spectrometry applying online Paternò–Büchi reaction

“…Precursors for higher-energy C-trap dissociation (HCD) by the Q Exactive plus mass spectrometer were dynamically selected by means of an inclusion list, which was generated by MZmine 2.34 [69,70] and contained a database of potential HAA species and their corresponding PB products, in a range of 16 to 32 carbon atoms and 0 to 2 double bonds in both acyl chains combined.…”

Toward a Standardized Strategy of Clinical Metabolomics for the Advancement of Precision Medicine

“…Having such a platform would improve the depth of upcoming studies effortlessly and improve the reproducibility of the results. MZmine 2, MS-DIAL, and the "all-in-one" cloud-based platform of XCMS/METLIN and its variants including XCMS-MRM are among the most typical examples of the openness and complement of computational pre-processing procedures in metabolomics [90,[94][95][96][97][98][99][100][101][102]. Notwithstanding, despite being the most popular statistical analysis tool used by the omics community, it still lacks functionality and is not particularly suitable for large-scale clinical metabolomics studies.…”