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Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry

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  • Benjamin C. Orsburn

    (The Johns Hopkins University)

  • Yuting Yuan

    (The Johns Hopkins University)

  • Namandjé N. Bumpus

    (The Johns Hopkins University)

Abstract

Single cell proteomics is a powerful tool with potential for markedly enhancing understanding of cellular processes. Here we report the development and application of multiplexed single cell proteomics using trapped ion mobility time-of-flight mass spectrometry. When employing a carrier channel to improve peptide signal, this method allows over 40,000 tandem mass spectra to be acquired in 30 min. Using a KRASG12C model human-derived cell line, we demonstrate the quantification of over 1200 proteins per cell with high relative sequence coverage permitting the detection of multiple classes of post-translational modifications in single cells. When cells were treated with a KRASG12C covalent inhibitor, this approach revealed cell-to-cell variability in the impact of the drug, providing insight missed by traditional proteomics. We provide multiple resources necessary for the application of single cell proteomics to drug treatment studies including tools to reduce cell cycle linked proteomic effects from masking pharmacological phenotypes.

Suggested Citation

  • Benjamin C. Orsburn & Yuting Yuan & Namandjé N. Bumpus, 2022. "Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34919-w
    DOI: 10.1038/s41467-022-34919-w
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    1. Erwin M. Schoof & Benjamin Furtwängler & Nil Üresin & Nicolas Rapin & Simonas Savickas & Coline Gentil & Eric Lechman & Ulrich auf dem Keller & John E. Dick & Bo T. Porse, 2021. "Quantitative single-cell proteomics as a tool to characterize cellular hierarchies," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
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