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

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 as a major advance in overall sensitivity. NanoPOTS dramatically enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive LC-MS, nanoPOTS allows identification of ~1500 to ~3,000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins were consistently identified from as few as 10 cells. Furthermore, we demonstrate robust 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.

Authors:
; ORCiD logo; ; ORCiD logo; ; ; ; ORCiD logo; ; ; ORCiD logo; ORCiD logo; ORCiD logo
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
1433774
Report Number(s):
PNNL-SA-125235
Journal ID: ISSN 2041-1723; 49682; 453040220
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
Environmental Molecular Sciences Laboratory

Citation Formats

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, and Kelly, Ryan T. Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells. United States: N. p., 2018. Web. doi:10.1038/s41467-018-03367-w.
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. Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells. United States. doi:10.1038/s41467-018-03367-w.
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, and Kelly, Ryan T. Wed . "Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells". United States. doi:10.1038/s41467-018-03367-w.
@article{osti_1433774,
title = {Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells},
author = {Zhu, Ying and Piehowski, Paul D. and Zhao, Rui and Chen, Jing and Shen, Yufeng and Moore, Ronald J. and Shukla, Anil K. and Petyuk, Vladislav A. and Campbell-Thompson, Martha and Mathews, Clayton E. and Smith, Richard D. and Qian, Wei-Jun and Kelly, Ryan T.},
abstractNote = {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 as a major advance in overall sensitivity. NanoPOTS dramatically enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive LC-MS, nanoPOTS allows identification of ~1500 to ~3,000 proteins from ~10 to ~140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins were consistently identified from as few as 10 cells. Furthermore, we demonstrate robust 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.},
doi = {10.1038/s41467-018-03367-w},
journal = {Nature Communications},
issn = {2041-1723},
number = 1,
volume = 9,
place = {United States},
year = {2018},
month = {2}
}

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