Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell
Abstract
Here, we report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions for more effective MS analysis of multiply charged peptides, resulting in an average of 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3 times more identifications than without FAIMS and a far greater level of proteome coverage for single mammalian cells than has been previously reported for a label-free study. Differential analysis of single microdissected motor neurons and interneurons from human spinal tissue indicated a similar level of proteome coverage, and the two subpopulations of cells were readily differentiated based on single-cell label-free quantification.
- Authors:
-
[1];
[4];
[5]
- Brigham Young Univ., Provo, UT (United States)
- Thermo Fisher Scientific, San Jose, CA (United States)
- Biogen, Inc., Cambridge, MA (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Brigham Young Univ., Provo, UT (United States); Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Publication Date:
- Research Org.:
- Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH)
- OSTI Identifier:
- 1770581
- Report Number(s):
- PNNL-SA-153571
Journal ID: ISSN 2041-6520
- Grant/Contract Number:
- AC05-76RL01830; R33CA225248; R01GM138931
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Chemical Science
- Additional Journal Information:
- Journal Volume: 12; Journal Issue: 3; Journal ID: ISSN 2041-6520
- Publisher:
- Royal Society of Chemistry
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Citation Formats
Cong, Yongzheng, Motamedchaboki, Khatereh, Misal, Santosh A., Liang, Yiran, Guise, Amanda J., Truong, Thy, Huguet, Romain, Plowey, Edward D., Zhu, Ying, Lopez-Ferrer, Daniel, and Kelly, Ryan T. Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell. United States: N. p., 2020.
Web. doi:10.1039/d0sc03636f.
Cong, Yongzheng, Motamedchaboki, Khatereh, Misal, Santosh A., Liang, Yiran, Guise, Amanda J., Truong, Thy, Huguet, Romain, Plowey, Edward D., Zhu, Ying, Lopez-Ferrer, Daniel, & Kelly, Ryan T. Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell. United States. https://doi.org/10.1039/d0sc03636f
Cong, Yongzheng, Motamedchaboki, Khatereh, Misal, Santosh A., Liang, Yiran, Guise, Amanda J., Truong, Thy, Huguet, Romain, Plowey, Edward D., Zhu, Ying, Lopez-Ferrer, Daniel, and Kelly, Ryan T. Tue .
"Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell". United States. https://doi.org/10.1039/d0sc03636f. https://www.osti.gov/servlets/purl/1770581.
@article{osti_1770581,
title = {Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell},
author = {Cong, Yongzheng and Motamedchaboki, Khatereh and Misal, Santosh A. and Liang, Yiran and Guise, Amanda J. and Truong, Thy and Huguet, Romain and Plowey, Edward D. and Zhu, Ying and Lopez-Ferrer, Daniel and Kelly, Ryan T.},
abstractNote = {Here, we report on the combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer for greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions for more effective MS analysis of multiply charged peptides, resulting in an average of 1056 protein groups identified from single HeLa cells without MS1-level feature matching. This is 2.3 times more identifications than without FAIMS and a far greater level of proteome coverage for single mammalian cells than has been previously reported for a label-free study. Differential analysis of single microdissected motor neurons and interneurons from human spinal tissue indicated a similar level of proteome coverage, and the two subpopulations of cells were readily differentiated based on single-cell label-free quantification.},
doi = {10.1039/d0sc03636f},
journal = {Chemical Science},
number = 3,
volume = 12,
place = {United States},
year = {Tue Nov 17 00:00:00 EST 2020},
month = {Tue Nov 17 00:00:00 EST 2020}
}
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