Paul Hutchins manuscript, LipiDex: an integrated software package for high-confidence lipid identification, received numerous positive reviews and was recently published in Cell Systems. According to Paul, “we built LipiDex to automate much of the tedious manual verification required to generate high-confidence lipidomics datasets from diverse sample types and instrument platforms.” Read the abstract below:
State-of-the-art proteomics software routinely quantifies thousands of peptides per experiment with minimal need for manual validation or processing of data. For the emerging field of discovery lipidomics via liquid chromatography tandem mass spectrometry (LC-MS/MS), comparably mature informatics tools do not exist. Here we introduce LipiDex, a freely available software suite which unifies and automates all stages of lipid identification, reducing hands-on processing time from hours to minutes for even the most expansive data sets. LipiDex utilizes flexible in-silico fragmentation templates and lipid-optimized MS/MS spectral matching routines to confidently identify and track hundreds of lipid species and unknown compounds from diverse sample matrices. Unique spectral and chromatographic peak purity algorithms accurately quantify co-isolation and co-elution of isobaric lipids, generating identifications which match the structural resolution afforded by the LC-MS/MS experiment. During final data filtering, ionization artifacts are removed to significantly reduce dataset redundancy. LipiDex interfaces with several LC-MS/MS software packages making robust lipid identification readily incorporated into pre-existing data workflows.