Untargeted Lipidomics Using Q Exactive Plus MS

Untargeted lipidomics was performed at the Harvard Center for Mass Spectrometry following a published protocol (Zhang et al., 2019 (link)). Data were acquired in MS/DD–MS² (top5) mode on a Q Exactive Plus quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific) online with an Ultimate 3000 HPLC (Thermo Fisher Scientific). Positive and negative ionization modes were acquired separately. Raw files (.raw) were converted into .mzXML via msconvert (Chambers et al., 2012 (link)) and analyzed in R using the XCMS package (Smith et al., 2006 (link)). The identified lipid species were verified manually in using Xcalibur (Thermo Fisher Scientific), taking into account MS¹ and MS² data.

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Zhang T., Alonzo I., Stubben C., Geng Y., Herdman C., Chandler N., Doane K.P., Pluimer B.R., Trauger S.A, & Peterson R.T. (2023). A zebrafish model of combined saposin deficiency identifies acid sphingomyelinase as a potential therapeutic target. Disease Models & Mechanisms, 16(7), dmm049995.

Publication 2023

Q Exactive Plus quadrupole-orbitrap mass spectrometer Ultimate 3000 HPLC Xcalibur

Hplc Lipid

Corresponding Organization :

Other organizations : University of Utah, Huntsman Cancer Institute, Harvard University

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Variable analysis

independent variables

Ionization mode (positive and negative)

dependent variables

Identified lipid species

control variables

Published protocol (Zhang et al., 2019)
Q Exactive Plus quadrupole-orbitrap mass spectrometer (Thermo Fisher Scientific)
Ultimate 3000 HPLC (Thermo Fisher Scientific)
XCMS package (Smith et al., 2006) for data analysis
Xcalibur (Thermo Fisher Scientific) for manual verification of identified lipid species

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