A DMS Shotgun Lipidomics Workflow Application to Facilitate High-Throughput, Comprehensive Lipidomics

Differential
mobility spectrometry (DMS) is highly useful for shotgun
lipidomic analysis because it overcomes difficulties in measuring
isobaric species within a complex lipid sample and allows for acyl
tail characterization of phospholipid species. Despite these advantages,
the resulting workflow presents technical challenges, including the
need to tune the DMS before every batch to update compensative voltages
settings within the method. The Sciex Lipidyzer platform uses a Sciex
5500 QTRAP with a DMS (SelexION), an LC system configured for direction
infusion experiments, an extensive set of standards designed for quantitative
lipidomics, and a software package (Lipidyzer Workflow Manager) that
facilitates the workflow and rapidly analyzes the data. Although the
Lipidyzer platform remains very useful for DMS-based shotgun lipidomics,
the software is no longer updated for current versions of Analyst
and Windows. Furthermore, the software is fixed to a single workflow
and cannot take advantage of new lipidomics standards or analyze additional
lipid species. To address this multitude of issues, we developed Shotgun
Lipidomics Assistant (SLA), a Python-based application that facilitates
DMS-based lipidomics workflows. SLA provides the user with flexibility
in adding and subtracting lipid and standard MRMs. It can report quantitative
lipidomics results from raw data in minutes, comparable to the Lipidyzer
software. We show that SLA facilitates an expanded lipidomics analysis
that measures over 1450 lipid species across 17 (sub)­classes. Lastly,
we demonstrate that the SLA performs isotope correction, a feature
that was absent from the original software.