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Shotgun Lipidomics Assistant: An open-source application to facilitate high-throughput, comprehensive lipidomics

The Sciex Lipidyzer platform bundles instrumentation, lipid standards and a software package that facilitates a lipidomics workflow. The platform was shown to be quantitative and consistently accurate across laboratories, while providing exceptional coverage of the mammalian plasma lipidome. However, the software portion of the platform is severely limited and is no longer being sold by Sciex. In response to these software needs, we developed Shotgun Lipidomics Assistant (SLA), an open-source Python-based application that facilitates DMS-based lipidomics workflows. The SLA utilizes a GUI interface and a set of simple Excel templates to facilitate each step in DMS-based shotgun lipidomics workflow. The SLA application can re-analyze data generated by the Lipidyzer software to produce identical results. Using the SLA, we’ve established an expanded lipidomics assay that measures over 1450 lipid species across 17 subclasses, over 400 more lipid species than the original Lipidyzer method. Further, we demonstrate the SLAs capability to perform isotope correction; a feature that was absent from the original Lipidyzer software. Lastly, we use the SLA to compare lipidomics data generated by DMS shotgun lipidomics on the Sciex 5500 and 6500+, as well as a HILIC lipidomics run performed on the Sciex 6500+ and 7500.