MobiLipid: A Tool for Enhancing CCS Quality Control of Ion Mobility–Mass Spectrometry Lipidomics by Internal Standardization

Ion mobility–mass
spectrometry (IM-MS) offers benefits for
lipidomics by obtaining IM-derived collision cross sections (CCS),
a conditional property of an ion that can enhance lipid identification.
While drift tube (DT) IM-MS retains a direct link to the primary experimental
method to derive CCS values, other IM technologies rely solely on
external CCS calibration, posing challenges due to dissimilar chemical
properties between lipids and calibrants. To address this, we introduce
MobiLipid, a novel tool facilitating the CCS quality control of IM-MS
lipidomics workflows by internal standardization. MobiLipid utilizes
a newly established DTCCSN2 library for uniformly
(U)13C-labeled lipids, derived from a U13C-labeled
yeast extract, containing 377 DTCCSN2 values.
This automated open-source R Markdown tool enables internal monitoring
and straightforward compensation for CCSN2 biases. It supports
lipid class- and adduct-specific CCS corrections, requiring only three
U13C-labeled lipids per lipid class-adduct combination
across 10 lipid classes without requiring additional external measurements.
The applicability of MobiLipid is demonstrated for trapped IM (TIM)-MS
measurements of an unlabeled yeast extract spiked with U13C-labeled lipids. Monitoring the CCSN2 biases of TIMCCSN2 values compared to DTCCSN2 library entries utilizing MobiLipid resulted in mean absolute
biases of 0.78% and 0.33% in positive and negative ionization mode,
respectively. By applying the CCS correction integrated into the tool
for the exemplary data set, the mean absolute CCSN2 biases
of 10 lipid classes could be reduced to approximately 0%.