Single-Cell Classification Using Mass Spectrometry through Interpretable Machine Learning

The brain consists of organized ensembles of cells that exhibit distinct morphologies, cellular connectivity, and dynamic biochemistries that control the executive functions of an organism. However, the relationships between chemical heterogeneity, cell function, and phenotype are not always understood. Recent advancements in matrix-assisted laser desorption/ionization mass spectrometry have enabled the high-throughput, multiplexed chemical analysis of single cells, capable of resolving hundreds of molecules in each mass spectrum. We developed a machine learning workflow to classify single cells according to their mass spectra based on cell groups of interest (GOI), e.g., neurons vs astrocytes. Three data sets from various cell groups were acquired on three different mass spectrometer platforms representing thousands of individual cell spectra that were collected and used to validate the single cell classification workflow. The trained models achieved >80% classification accuracy and were subjected to the recently developed instance-based model interpretation framework, SHapley Additive exPlanations (SHAP), which locally assigns feature importance for each single-cell spectrum. SHAP values were used for both local and global interpretations of our data sets, preserving the chemical heterogeneity uncovered by the single-cell analysis while offering the ability to perform supervised analysis. The top contributing mass features to each of the GOI were ranked and selected using mean absolute SHAP values, highlighting the features that are specific to the defined GOI. Our approach provides insight into discriminating the chemical profiles of the single cells through interpretable machine learning, facilitating downstream analysis and validation.