Quality Control Standards for Batch Effect Evaluation and Correction in Mass Spectrometry Imaging

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) allows spatial molecular profiling. Despite many successful applications, an appropriate control of technical variations is still lacking for result reproducibility assessment and for maximizing the MSI data quality. To address this, we introduce a novel quality control standard (QCS) design and data analysis pipeline accounting for variability due to sample preparation and instrument performance. Firstly, we created a tissue mimicking QCS consisting of propranolol in a gelatin matrix. We showed that this QCS mimics ion suppression of propranolol in the tissue. Next, a three-day batch experiment demonstrated the QCS's performance to longitudinal technical variations, establishing it as an effective indicator of batch effects. Then three computational approaches for batch effect correction were applied for the first time to MALDI-MSI data, leading to a significant reduction of QCS variation and to improved sample clustering by using multivariate principal component analysis. Altogether, we offer the designed QCS in combination with a data correction pipeline for MALDI-MSI users for batch effect evaluation and correction.