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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:
 [1]; ORCiD logo [2];  [1]; ORCiD logo [3];  [2];  [2];  [2]; ORCiD logo [2];  [3];  [3]; ORCiD logo [2]; ORCiD logo [2]; ORCiD logo [1]
+ Show Author Affiliations
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
  3. Univ. of Florida, Gainesville, FL (United States). Dept. of Pathology, Immunology and Laboratory Medicine
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH)
OSTI Identifier:
1432521
Alternate Identifier(s):
OSTI ID: 1513201
Report Number(s):
PNNL-SA-125235
Journal ID: ISSN 2041-1723; PII: 3367
Grant/Contract Number:  
AC05-76RL01830; R21 EB020976; R33 CA225248; P41 GM103493; UC4 DK104167; DP3 DK110844; 1S10OD016350-01
Resource Type:
Accepted Manuscript
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:
59 BASIC BIOLOGICAL SCIENCES

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.
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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. https://doi.org/10.1038/s41467-018-03367-w
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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. https://doi.org/10.1038/s41467-018-03367-w. https://www.osti.gov/servlets/purl/1432521.
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@article{osti_1432521,
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},
number = 1,
volume = 9,
place = {United States},
year = {Wed Feb 28 00:00:00 EST 2018},
month = {Wed Feb 28 00:00:00 EST 2018}
}
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SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities
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Heterogeneity and Lobularity of Pancreatic Pathology in Type 1 Diabetes during the Prediabetic Phase
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  • Rodriguez-Calvo, Teresa; Suwandi, Jessica S.; Amirian, Natalie
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