posted on 2024-01-04, 20:34authored byKanako Tokiyoshi, Yuki Matsuzawa, Mikiko Takahashi, Hiroaki Takeda, Mayu Hasegawa, Junki Miyamoto, Hiroshi Tsugawa
Untargeted lipidomics using liquid
chromatography (LC)
coupled
with tandem mass spectrometry (MS) is essential for large cohort studies.
Using a fast LC gradient of less than 10 min for the rapid screening
of lipids decreases the annotation rate, because of the lower coverage
of the MS/MS spectra caused by the narrow peak width. A systematic
procedure is proposed in this study to achieve a high annotation rate
in fast LC-based untargeted lipidomics by integrating data-dependent
acquisition (DDA) and sequential window acquisition of all-theoretical
mass spectrometry data-independent acquisition (SWATH-DIA) techniques
using the updated MS-DIAL program. This strategy uses variable SWATH-DIA
methods for quality control (QC) samples, which are a mixture of biological
samples that were analyzed multiple times to correct the MS signal
drift. In contrast, biological samples are analyzed using DDA to facilitate
the structural elucidation of lipids using the pure spectrum to the
maximum extent. The workflow is demonstrated using an 8.6 min LC gradient,
where the QC samples are analyzed using five different SWATH-DIA methods.
The use of both DDA and SWATH-DIA achieves a 1.7-fold annotation coverage
from publicly available benchmark data obtained using a fast LC-DDA-MS
technique and offers 95.3% lipid coverage, as compared to the benchmark
data set from a 25 min LC gradient. This study demonstrates that harmonized
improvements in analytical conditions and informatics tools provide
a comprehensive lipidome in fast LC-based untargeted lipidomics, not
only for large-scale studies but also for small-scale experiments,
contributing to both clinical applications and basic biology.