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Nat Commun. 2018 Feb 28;9(1):882. doi: 10.1038/s41467-018-03367-w.

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

Author information

1
The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
2
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
3
Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32611, USA.
4
The Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA. ryan.kelly@pnnl.gov.

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.

PMID:
29491378
PMCID:
PMC5830451
DOI:
10.1038/s41467-018-03367-w
[Indexed for MEDLINE]
Free PMC Article

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