Impact of Local Air Pressure on Ion Mobilities and Data Consistency in diaPASEF-Based High Throughput Proteomics

Data-independent acquisition (DIA) on ion mobility mass
spectrometers
enables deep proteome coverage and high data completeness in large-scale
proteomics studies. For advanced acquisition schemes such as parallel
accumulation serial fragmentation-based DIA (diaPASEF) stability of
ion mobility (1/K0) over time is crucial for consistent
data quality. We found that minor changes in environmental air pressure
systematically affect the vacuum pressure in the TIMS analyzer, causing
ion mobility shifts. By comparing experimental ion mobilities with
historical weather data, we attributed observed drifts to fluctuations
in the ground air pressure. Moderate air pressure changes of e.g.
fifteen mbar induce ion mobility shifts of 0.025 Vs/cm2. These drifts negatively impact peptide quantification across consecutively
acquired samples due to drift-dependent abundance changes and increased
missing values for ions located at the boundaries of diaPASEF isolation
windows, which cannot be corrected by postprocessing. To address this,
we applied an in-batch mobility autocalibration feature on a run-wise
basis, leading to full elimination of ion mobility drifts.