Comparative Lipidomics of Caenorhabditis elegans Metabolic Disease Models by SWATH Non-Targeted Tandem Mass Spectrometry

Abstract

Tandem mass spectrometry (MS/MS) with Sequential Window Acquisition of all Theoretical (SWATH) mass spectra generates a comprehensive archive of lipid species within an extract for retrospective, quantitative MS/MS analysis. Here we apply this new technology in Caenorhabditis elegans (C. elegans) to identify potential lipid mediators and pathways. The DAF-1 type I TGF-β and DAF-2 insulin receptors transmit endocrine signals that couple metabolic status to fertility and lifespan. Mutations in daf-1 and daf-2 reduce prostaglandin-endoperoxide synthase (i.e., Cox)-independent prostaglandin synthesis, increase triacylglyceride storage, and alter transcription of numerous lipid metabolism genes. However, the extent to which DAF-1 and DAF-2 signaling modulate lipid metabolism and the underlying mechanisms are not well understood. MS/MSALL with SWATH analysis across the groups identified significant changes in numerous lipids, including specific triacylglycerols, diacylglycerols, and phosphatidylinositols. Examples are provided, using retrospective neutral loss and precursor ion scans as well as MS/MS spectra, to help identify annotated lipids and search libraries for lipids of interest. As proof of principle, we used comparative lipidomics to investigate the prostaglandin metabolism pathway. SWATH data support an unanticipated model: Cox-independent prostaglandin synthesis may involve lysophosphatidylcholine and other lyso glycerophospholipids. This study showcases the power of comprehensive, retrospectively searchable lipid archives as a systems approach for biological discovery in genetic animal models.

Comprehensive shotgun lipidomics of human meibomian gland secretions using MS/MSall with successive switching between acquisition polarity modes

“…The MS/MS all approach combines the comprehensiveness of full-scan MS and MS/MS analyses with the high-detection sensitivity for specific classes of lipids of interest associated with various pseudo-PIS (pPIS) and pseudo-NLS (pNLS) detection methods (29)(30)(31)(32)(33). In addition to the product ions analyzed in pPIS and pNLS, other product ion information is also available to confirm assignments.…”

Mass spectrometric evidence for the modification of small molecules in a cobalt‐60‐irradiated rodent diet

“…During MS/MS ALL acquisition, precursor ion isolation windows of 1.2 Da width selected in Q1 are fragmented in the Q2 collision cell and the generated product ions are monitored at high mass resolution by the time-of-flight analyzer. The MS/MS ALL data included a 250ms survey scan of time-of-flight MS data from m/z 200 to 1200, followed by collection of 1000 MS/MS spectra of the selected mass windows [7] . The collision energy was set to 35 V, curtain gas to 20, GS1 and GS2 to 15, spray voltage to 5500 V (positive ion mode)/ 4500 V (negative ion mode), and temperature to 400°C.…”

SWATH‐MS as a tool for biomarker discovery: From basic research to clinical applications

“…The major focus of this review is the SWATH‐MS application in proteomics, however SWATH‐MS has been also applied to the analysis of low molecular weight compounds (LMWC) , expanding the concepts of compound libraries and samples digital maps to the analysis of other biomolecules rather than proteins. Although, contrary to what is observable in the case of proteomics analysis, the SWATH‐MS has shown to be beneficial even for compound identification from SWATH acquisition file , presenting better results when compared with either DDA experiments or other DIA methods .…”