U.S. Department of Energy

Pacific Northwest National Laboratory

Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells

TitleNanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells
Publication TypeJournal Article
Year of Publication2018
AuthorsZhu Y., Piehowski P.D, Zhao R., Chen J., Shen Y., Moore R.J, Shukla A.K, Petyuk V.A, Campbell-Thompson M., Mathews C.E, Smith R.D, Qian W.J, Kelly R.T
JournalNat Commun
Abstract

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of  1500 to  3000 proteins from  10 to  140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of  2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.

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