Lipid and Metabolite Annotation Using Lipid Data Analyzer.

The Lipid Data Analyzer (LDA) is a platform-independent software tool for the automated identification and quantification of lipid species and other metabolites in both untargeted and targeted mass spectrometry (MS) data. LDA mirrors the decision-making process of trained MS experts, enabling automated, high-throughput analyses across any instrumental setup through customizable, rule-based logic. These decision rule sets represent chemical and structural logic, yielding annotation results of high reliability. Furthermore, decision rules can be easily extended to accommodate new lipid classes, adduct forms, or fragmentation mechanisms. This makes LDA particularly effective for identifying novel lipid species or structural isomers that are often missed by traditional approaches, and enables users without a bioinformatics background to easily adapt to evolving analytical protocols. Moreover, LDA supports the identification of double bond positions and other modifications, such as oxidations. Here, we present a step-by-step guide and practical tips for efficient operation of LDA, and provide an introductory discussion of common pitfalls in lipidomics data analysis.