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

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 proc...

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Published in:Nature communications Vol. 9; no. 1; pp. 882 - 10
Main Authors: Zhu, Ying, Piehowski, Paul D., Zhao, Rui, Chen, Jing, Shen, Yufeng, Moore, Ronald J., Shukla, Anil K., Petyuk, Vladislav A., Campbell-Thompson, Martha, Mathews, Clayton E., Smith, Richard D., Qian, Wei-Jun, Kelly, Ryan T.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 28.02.2018
Nature Publishing Group
Nature Portfolio
Subjects:
631/1647/2067
631/1647/296
82/16
82/58
82/62
82/80
BASIC BIOLOGICAL SCIENCES
Biomedical materials
Depth profiling
Diabetes mellitus
Gene Expression Profiling
Humanities and Social Sciences
Humans
Islets of Langerhans - chemistry
Islets of Langerhans - metabolism
Liquid chromatography
Mammalian cells
Mass Spectrometry
Mass spectroscopy
multidisciplinary
Pancreas
Proteins
Proteins - chemistry
Proteins - genetics
Proteins - metabolism
Proteome - chemistry
Proteome - genetics
Proteome - metabolism
Proteomics
Science
Science (multidisciplinary)
ISSN:2041-1723, 2041-1723
Online Access:Get full text
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Summary: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. There is a great need of developing highly sensitive mass spectrometry-based proteomics analysis for small cell populations. Here, the authors establish a robotically controlled chip-based nanodroplet processing platform and demonstrate its ability to profile the proteome from 10–100 mammalian cells.
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AC05-76RL01830; R21 EB020976; R33 CA225248; P41 GM103493; UC4 DK104167; DP3 DK110844; 1S10OD016350-01
USDOE
PNNL-SA-125235
National Institutes of Health (NIH)
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-018-03367-w