Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering

Woo, Jongmin; Clair, Geremy C. D.; Williams, Sarah M.; Feng, Song; Tsai, Chia-Feng; Moore, Ronald J.; Chrisler, William B.; Smith, Richard D.; Kelly, Ryan T.; Paša-Tolić, Ljiljana; Ansong, Charles; Zhu, Ying

doi:10.1016/j.cels.2022.02.003

DOE OSTI · 2282559

Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering

Woo, Jongmin·Clair, Geremy C. D.·Williams, Sarah M.·Feng, Song·Tsai, Chia-Feng·Moore, Ronald J.·Chrisler, William B.·Smith, Richard D.·Kelly, Ryan T.·Paša-Tolić, Ljiljana·Ansong, Charles·Zhu, Ying

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Abstract

Single-cell proteomics (scProteomics) promises to advance our understanding of cell functions within complex biological systems. However, a major challenge of current methods is their inability to identify and provide accurate quantitative information for low abundance proteins. Herein, we describe an ion mobility-enhanced mass spectrometry acquisition and peptide identification method, TIFF (Transferring Identification based on FAIMS Filtering), to improve the sensitivity and accuracy of label-free scProteomics. TIFF extends the ion accumulation times for peptide ions by filtering out singly charged ions. The peptide identities are assigned by a three-dimensional MS1 feature matching approach (retention time, accurate mass, and FAIMS compensation voltage). TIFF method enabled unbiased proteome analysis to a depth of >1,700 proteins in single HeLa cells with >1,100 proteins consistently identified. As a demonstration, we applied the TIFF method to obtain temporal proteome profiles of >150 single murine macrophage cells during lipopolysaccharide stimulation and identified time-dependent proteome changes.

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59 BASIC BIOLOGICAL SCIENCES FAIMS analytical detection method feature matching ion mobility low-abundance proteins lung macrophage activation mass spectrometry nanoPOTS single-cell proteomics three-dimensional

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Woo, Jongmin, Clair, Geremy C. D., Williams, Sarah M., Feng, Song, Tsai, Chia-Feng, Moore, Ronald J., Chrisler, William B., Smith, Richard D., Kelly, Ryan T., Paša-Tolić, Ljiljana, Ansong, Charles, Zhu, Ying. 2022-03-16. Three-dimensional feature matching improves coverage for single-cell proteomics based on ion mobility filtering. https://doi.org/10.1016/j.cels.2022.02.003

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