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Title: High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform

Abstract

Effective extension of mass spectrometry-based proteomics to single cells remains challenging. Herein we combined microfluidic nanodroplet technology with tandem mass tag (TMT) isobaric labeling to significantly improve analysis throughput and proteome coverage for single mammalian cells. Isobaric labeling facilitated multiplex analysis of single cell-sized protein quantities to a depth of ~1,600 proteins with median CV of 10.9% and correlation coefficient of 0.98. To demonstrate in-depth high throughput single cell analysis, the platform was applied to measure protein expression in 72 single cells from three murine cell populations (epithelial, immune, and endothelial cells) in <2 days instrument time with over 2,300 proteins identified. Principal component analysis grouped the single cells into three distinct populations based on protein expression with each population characterized by well-known cell-type specific markers. Our platform enables high throughput and unbiased characterization of single cell heterogeneity at the proteome level.

Authors:
 [1]; ORCiD logo [1];  [1];  [1];  [1];  [1];  [1];  [1]; ORCiD logo [1];  [1]; ORCiD logo [1];  [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [1]; ORCiD logo [1]
  1. BATTELLE (PACIFIC NW LAB)
  2. BRIGHAM YOUNG UNIVERSITY
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1608534
Report Number(s):
PNNL-SA-146297
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Analytical Chemistry
Additional Journal Information:
Journal Volume: 91; Journal Issue: 20
Country of Publication:
United States
Language:
English

Citation Formats

Dou, Maowei, Clair, Geremy CD, Tsai, Chia-Feng, Xu, Kerui, Chrisler, William B., Sontag, Ryan L., Zhao, Rui, Moore, Ronald J., Liu, Tao, Pasa-Tolic, Ljiljana, Smith, Richard D., Shi, Tujin, Adkins, Joshua N., Qian, Weijun, Kelly, Ryan T., Ansong, Charles K., and Zhu, Ying. High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform. United States: N. p., 2019. Web. doi:10.1021/acs.analchem.9b03349.
Dou, Maowei, Clair, Geremy CD, Tsai, Chia-Feng, Xu, Kerui, Chrisler, William B., Sontag, Ryan L., Zhao, Rui, Moore, Ronald J., Liu, Tao, Pasa-Tolic, Ljiljana, Smith, Richard D., Shi, Tujin, Adkins, Joshua N., Qian, Weijun, Kelly, Ryan T., Ansong, Charles K., & Zhu, Ying. High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform. United States. doi:10.1021/acs.analchem.9b03349.
Dou, Maowei, Clair, Geremy CD, Tsai, Chia-Feng, Xu, Kerui, Chrisler, William B., Sontag, Ryan L., Zhao, Rui, Moore, Ronald J., Liu, Tao, Pasa-Tolic, Ljiljana, Smith, Richard D., Shi, Tujin, Adkins, Joshua N., Qian, Weijun, Kelly, Ryan T., Ansong, Charles K., and Zhu, Ying. Tue . "High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform". United States. doi:10.1021/acs.analchem.9b03349.
@article{osti_1608534,
title = {High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform},
author = {Dou, Maowei and Clair, Geremy CD and Tsai, Chia-Feng and Xu, Kerui and Chrisler, William B. and Sontag, Ryan L. and Zhao, Rui and Moore, Ronald J. and Liu, Tao and Pasa-Tolic, Ljiljana and Smith, Richard D. and Shi, Tujin and Adkins, Joshua N. and Qian, Weijun and Kelly, Ryan T. and Ansong, Charles K. and Zhu, Ying},
abstractNote = {Effective extension of mass spectrometry-based proteomics to single cells remains challenging. Herein we combined microfluidic nanodroplet technology with tandem mass tag (TMT) isobaric labeling to significantly improve analysis throughput and proteome coverage for single mammalian cells. Isobaric labeling facilitated multiplex analysis of single cell-sized protein quantities to a depth of ~1,600 proteins with median CV of 10.9% and correlation coefficient of 0.98. To demonstrate in-depth high throughput single cell analysis, the platform was applied to measure protein expression in 72 single cells from three murine cell populations (epithelial, immune, and endothelial cells) in <2 days instrument time with over 2,300 proteins identified. Principal component analysis grouped the single cells into three distinct populations based on protein expression with each population characterized by well-known cell-type specific markers. Our platform enables high throughput and unbiased characterization of single cell heterogeneity at the proteome level.},
doi = {10.1021/acs.analchem.9b03349},
journal = {Analytical Chemistry},
number = 20,
volume = 91,
place = {United States},
year = {2019},
month = {10}
}