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bioRxiv · 10.1101/2024.10.22.618936

SLB-msSIM: a spectral library-based multiplex segmented SIM platform for single-cell proteomic analysis

Senavirathna, L.·Ma, C.·Duong, V. A.·Tsai, H.-Y.·Chen, R.·Pan, S.
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Abstract

Mass spectrometry (MS)-based single-cell proteomics, while highly challenging, offers unique potential for a wide range of applications to interrogate cellular heterogeneity, trajectories, and phenotypes at a functional level. We report here the development of the spectral library-based multiplex segmented selected ion monitoring (SLB-msSIM) method, a conceptually unique approach with significantly enhanced sensitivity and robustness for single-cell analysis. The single-cell MS data is acquired by multiplex segmented selected ion monitoring (msSIM) technique, which sequentially applies multiple isolation cycles with the quadrupole using 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 using a well-defined spectral library. We applied the SLB-msSIM method to interrogate cellular heterogeneity in various pancreatic cancer cell lines, revealing common and distinct functional traits among PANC-1, MIA-PaCa2, AsPc-1, HPAF, and normal HPDE cells. Furthermore, for the first time, our novel data revealed the diverse cell trajectories of individual PANC-1 cells during the induction and reversal of epithelial-mesenchymal transition (EMT). Collectively, our results demonstrate that SLB-msSIM is a highly sensitive and robust platform, applicable to a wide range of instruments for single-cell proteomic studies.

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Senavirathna, L., Ma, C., Duong, V. A., Tsai, H.-Y., Chen, R., Pan, S.. 2024-10-25. SLB-msSIM: a spectral library-based multiplex segmented SIM platform for single-cell proteomic analysis. https://doi.org/10.1101/2024.10.22.618936

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