Factorial-Design-Based Optimization of a Commercial MALDI-2 timsTOF Mass Spectrometer for Lipid Analysis

Matrix-assisted laser desorption/ionization mass spectrometry with laser postionization (MALDI-2 MS) has become an important technique for the analysis of a wide range of biomolecules. It has traditionally been limited to custom lab-built setups until the recent introduction of a commercial timsTOF fleX MALDI-2 system. A comprehensive optimization of the timsTOF fleX system for lipid analysis was performed using a factorial design of experiments (DOE). By examining 13 instrumental parameters across three full factorial DOEs, we performed over 1500 individual runs to assess the impact and cross interactions of these parameters on the lipid signal intensity. We found optimal values for both ion transmission and MALDI-2 parameters to maximize the signals within the lipid region. These results show that laser shot frequency, collision RF, and pre pulse storage were essential for enhancing lipid ion transmission, resulting in a nearly 5-fold increase in signal intensity compared to default parameters. For MALDI-2 optimization, positive and negative modes showed similar optimized values, with TIMS In pressure and laser power being crucial. Overall, optimization of ion optics and MALDI-2 resulted in signal enhancements of nearly 2 orders of magnitude for certain lipid species.