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

Journal of the American Society for Mass Spectrometry, vol. 32, pp. 2655–2663

Abstract

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 Although the Lipidyzer platform remains very useful for DMS-based shotgun lipidomics, the software is no longer updated for current versions of Analyst and Windows.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.

Authors 11

1. Baolong Su

   University of California, Los Angeles

   Affiliation as printed

   Department of Biological Chemistry, University of California, Los Angeles, California 90095, United States

   UCLA Lipidomics Laboratory, University of California, Los Angeles, California 90095, United States

2. Lisa Bettcher

   University of Washington

   Affiliation as printed

   Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States

3. Wei-Yuan Hsieh

   University of California, Los Angeles

   Affiliation as printed

   Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, United States

4. Daniel Hornburg

   Stanford Medicine · Stanford University

   Affiliation as printed

   Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, United States

5. Mackenzie Jo Pearson
   Affiliation as printed

   SCIEX, Redwood City, California 94065, United States

6. Niek Blomberg Aachen Center for Proteomics and Metabolomics

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, Netherlands

7. Martin A. Giera Aachen Center for Proteomics and Metabolomics

   Leiden University Medical Center

   Affiliation as printed

   Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333ZA Leiden, Netherlands

8. Michael Snyder

   Stanford Medicine · Stanford University

   Affiliation as printed

   Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, United States

9. Daniel Raftery

   University of Washington

   Affiliation as printed

   Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States

10. Steven J. Bensinger

    University of California, Los Angeles

    Affiliation as printed

    Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, California 90095, United States

    UCLA Lipidomics Laboratory, University of California, Los Angeles, California 90095, United States

11. Kevin J. Williams corresponding

    University of California, Los Angeles

    Affiliation as printed

    Department of Biological Chemistry, University of California, Los Angeles, California 90095, United States

    UCLA Lipidomics Laboratory, University of California, Los Angeles, California 90095, United States