Sep 29, 2025
Untargeted MS-based lipidomic analyses
- Maria Jose Perez J.1
- 1Institut Imagine
- Team Deleidi
Protocol Citation: Maria Jose Perez J. 2025. Untargeted MS-based lipidomic analyses. protocols.io https://dx.doi.org/10.17504/protocols.io.x54v95kjml3e/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 25, 2025
Last Modified: September 29, 2025
Protocol Integer ID: 228170
Keywords: based lipidomic analysis, based lipidomic, untargeted m
Funders Acknowledgements:
ASAP
Abstract
Untargeted MS-based lipidomic analyses
Troubleshooting
Collect iPSC-derived microglia and prepare cell pellets. Flash-freeze cell pellets to be shipped on dry ice (our pellets were sent to Lipotype Gmbh, Dresden, Germany)
Samples were processed using a modified chloroform/methanol extraction protocol with internal standards specific to each lipid class (Ref. main text Surma et al., 2021).
Lipid extracts were analyzed on a Q Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific) equipped with a Triversa Nanomate automated nano-ESI source.
Measurements were performed in both positive and negative ion modes.
External mass calibration was conducted weekly to maintain <5 ppm mass accuracy.
Lipids were identified using LipotypeXplorer software based on MS1 and MS/MS data.
Quantification data were normalized to internal standards, and data were reported in both pmol and mol% formats
Lipid species with signal intensities ≥5-fold above blank and noise thresholds were retained.
Reproducibility was confirmed using quality control samples (mammalian blood) with a median coefficient of variation (CV) of ~4%.