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Orbitrap Collision Cross Section Measurements Enhance Isomer Annotations in Lipidomics
Ziqin Ni1, Konstantin Ayzikov2, Alexander Makarov2
1School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.
Biorxiv : the Preprint Server for Biology
|July 10, 2026
Summary
A new method infers lipid collision cross section (CCS) values from Orbitrap mass spectrometry, overcoming challenges in lipid identification. This advance improves lipidomics accuracy and accelerates structural analysis in complex biological samples.
Area of Science:
- Analytical Chemistry
- Lipidomics
- Mass Spectrometry
Background:
- High-resolution mass spectrometry (HRMS) faces challenges in confident lipid annotation due to lipidome diversity and isomeric species.
- Ion mobility collision cross section (CCS) measurements offer structural insights but are not universally available on all HRMS platforms.
- Existing HRMS platforms often require a trade-off between mass resolution, accuracy, and robustness for CCS measurements.
Purpose of the Study:
- To introduce a novel method for inferring lipid CCS values directly from liquid chromatography (LC)-Orbitrap MS experiments.
- To enable more reliable lipid annotation and accelerate structural elucidation in complex lipidomic studies.
- To provide a robust alternative for obtaining CCS information without specialized ion mobility instrumentation.
Main Methods:
- Development of the Orbi CCS method to infer lipid CCS values from Orbitrap mass analyzer pressure readings.
- Correction of CCS values for LC gradient solvent composition effects using post-column isotopically labeled internal standards.
- Validation of Orbi CCS accuracy and precision against established differential mobility spectrometry (DMS) and trapped ion mobility spectrometry (TIMS) CCS values.
Main Results:
- The Orbi CCS method successfully assigned CCS values to hundreds of lipid features in a single LC run.
- Achieved average precision better than 1% and accuracy of 1-2% relative to reference CCS values (DT CCS and TIMS CCS).
- Demonstrated that Orbitrap mass analyzer pressure is influenced by LC gradient solvent composition, necessitating correction.
Conclusions:
- The Orbi CCS method provides accurate and precise CCS measurements directly from LC-Orbitrap MS data.
- This approach enhances the reliability of lipid annotation in complex mixtures by matching experimental CCS values to reference databases.
- The method accelerates lipid structural elucidation by leveraging the combined information of CCS, retention time, and m/z.
