msSIM for single-cell proteomic analysis

We report the development of the spectral library-based multiplex segmented Selected Ion Monitoring (SLB-msSIM) method, a novel approach that significantly improves sensitivity and robustness for single-cell analysis. Single-cell MS data is acquired using the msSIM technique, which sequentially applies multiple isolation cycles with the quadrupole, utilizing a wide isolation window in each cycle to accumulate and store precursor ions in the C-trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching with a well-defined spectral library. We employed the SLB-msSIM method to explore cellular heterogeneity across multiple cell lines and to analyze cellular trajectories during epithelial-mesenchymal transition.