Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics

Chia Feng Tsai; Pengfei Zhang; David Scholten; Kendall Martin; Yi Ting Wang; Rui Zhao; William B. Chrisler; Dhwani B. Patel; Maowei Dou; Yuzhi Jia; Carolina Reduzzi; Xia Liu; Ronald J. Moore; Kristin E. Burnum-Johnson; Miao Hsia Lin; Chuan Chih Hsu; Jon M. Jacobs; Jacob Kagan; Sudhir Srivastava; Karin D. Rodland; H. Steven Wiley; Wei Jun Qian; Richard D. Smith; Ying Zhu; Massimo Cristofanilli; Tao Liu; Huiping Liu; Tujin Shi

doi:10.1038/s42003-021-01797-9

Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics

Chia Feng Tsai, Pengfei Zhang, David Scholten, Kendall Martin, Yi Ting Wang, Rui Zhao, William B. Chrisler, Dhwani B. Patel, Maowei Dou, Yuzhi Jia, Carolina Reduzzi, Xia Liu, Ronald J. Moore, Kristin E. Burnum-Johnson, Miao Hsia Lin, Chuan Chih Hsu, Jon M. Jacobs, Jacob Kagan, Sudhir Srivastava, Karin D. RodlandH. Steven Wiley, Wei Jun Qian, Richard D. Smith, Ying Zhu, Massimo Cristofanilli, Tao Liu, Huiping Liu, Tujin Shi

Research output: Contribution to journal › Article › peer-review

67 Scopus citations

Abstract

Large numbers of cells are generally required for quantitative global proteome profiling due to surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible for rare cell populations (e.g., circulating tumor cells (CTCs)). Here we report a surfactant-assisted one-pot sample preparation coupled with mass spectrometry (MS) method termed SOP-MS for label-free global single-cell proteomics. SOP-MS capitalizes on the combination of a MS-compatible nonionic surfactant, n-Dodecyl-β-D-maltoside, and hydrophobic surface-based low-bind tubes or multi-well plates for ‘all-in-one’ one-pot sample preparation. This ‘all-in-one’ method including elimination of all sample transfer steps maximally reduces surface adsorption losses for effective processing of single cells, thus improving detection sensitivity for single-cell proteomics. This method allows convenient label-free quantification of hundreds of proteins from single human cells and ~1200 proteins from small tissue sections (close to ~20 cells). When applied to a patient CTC-derived xenograft (PCDX) model at the single-cell resolution, SOP-MS can reveal distinct protein signatures between primary tumor cells and early metastatic lung cells, which are related to the selection pressure of anti-tumor immunity during breast cancer metastasis. The approach paves the way for routine, precise, quantitative single-cell proteomics.

Original language	English (US)
Article number	265
Journal	Communications Biology
Volume	4
Issue number	1
DOIs	https://doi.org/10.1038/s42003-021-01797-9
State	Published - Dec 2021

Funding

Portions of the research were supported by NIH R21CA223715 (to T.S.), NIH UG3CA256967 (to T.S. and H.L.), DOD BCRP W81XWH-16-1-0021 (to W.J.Q), American Cancer Society grant ACS127951-RSG-15-025-01-CSM (to H.L.), NIH R01CA245699 (to H.L.), DOD BC190982 (to H.L.), NIH P41GM103493 (to R.D.S.), R01DK122160 (to W.J.Q.), MOST109-2320-B-002-010 (to M.H.L), and NCI EDRN Interagency Agreement ACN15006-001 (to T.L. and K.D.R). The experimental work described herein was performed in the Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, a national scientific user facility sponsored by the United States of America Department of Energy under Contract DE-AC05-76RL0 1830. We thank M.J. Gaffrey, T. Zhang, T.L. Fillmore for generous assistance with experiments, A.K. Shukla for technical support in proteomics, Youbin Zhang for patient blood analysis on the CellSearch platform, Rokana Taftaf for assisting the IHC and flow analyses of PCDX-205, and Nathan Johnson for assistance with graphics.

ASJC Scopus subject areas

Medicine (miscellaneous)
General Biochemistry, Genetics and Molecular Biology
General Agricultural and Biological Sciences

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s42003-021-01797-9

Cite this

Tsai, C. F., Zhang, P., Scholten, D., Martin, K., Wang, Y. T., Zhao, R., Chrisler, W. B., Patel, D. B., Dou, M., Jia, Y., Reduzzi, C., Liu, X., Moore, R. J., Burnum-Johnson, K. E., Lin, M. H., Hsu, C. C., Jacobs, J. M., Kagan, J., Srivastava, S., ... Shi, T. (2021). Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics. Communications Biology, 4(1), Article 265. https://doi.org/10.1038/s42003-021-01797-9

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title = "Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics",

abstract = "Large numbers of cells are generally required for quantitative global proteome profiling due to surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible for rare cell populations (e.g., circulating tumor cells (CTCs)). Here we report a surfactant-assisted one-pot sample preparation coupled with mass spectrometry (MS) method termed SOP-MS for label-free global single-cell proteomics. SOP-MS capitalizes on the combination of a MS-compatible nonionic surfactant, n-Dodecyl-β-D-maltoside, and hydrophobic surface-based low-bind tubes or multi-well plates for {\textquoteleft}all-in-one{\textquoteright} one-pot sample preparation. This {\textquoteleft}all-in-one{\textquoteright} method including elimination of all sample transfer steps maximally reduces surface adsorption losses for effective processing of single cells, thus improving detection sensitivity for single-cell proteomics. This method allows convenient label-free quantification of hundreds of proteins from single human cells and ~1200 proteins from small tissue sections (close to ~20 cells). When applied to a patient CTC-derived xenograft (PCDX) model at the single-cell resolution, SOP-MS can reveal distinct protein signatures between primary tumor cells and early metastatic lung cells, which are related to the selection pressure of anti-tumor immunity during breast cancer metastasis. The approach paves the way for routine, precise, quantitative single-cell proteomics.",

author = "Tsai, {Chia Feng} and Pengfei Zhang and David Scholten and Kendall Martin and Wang, {Yi Ting} and Rui Zhao and Chrisler, {William B.} and Patel, {Dhwani B.} and Maowei Dou and Yuzhi Jia and Carolina Reduzzi and Xia Liu and Moore, {Ronald J.} and Burnum-Johnson, {Kristin E.} and Lin, {Miao Hsia} and Hsu, {Chuan Chih} and Jacobs, {Jon M.} and Jacob Kagan and Sudhir Srivastava and Rodland, {Karin D.} and {Steven Wiley}, H. and Qian, {Wei Jun} and Smith, {Richard D.} and Ying Zhu and Massimo Cristofanilli and Tao Liu and Huiping Liu and Tujin Shi",

note = "Publisher Copyright: {\textcopyright} 2021, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.",

year = "2021",

month = dec,

doi = "10.1038/s42003-021-01797-9",

language = "English (US)",

volume = "4",

journal = "Communications Biology",

issn = "2399-3642",

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Tsai, CF, Zhang, P, Scholten, D, Martin, K, Wang, YT, Zhao, R, Chrisler, WB, Patel, DB, Dou, M, Jia, Y, Reduzzi, C, Liu, X, Moore, RJ, Burnum-Johnson, KE, Lin, MH, Hsu, CC, Jacobs, JM, Kagan, J, Srivastava, S, Rodland, KD, Steven Wiley, H, Qian, WJ, Smith, RD, Zhu, Y, Cristofanilli, M, Liu, T, Liu, H & Shi, T 2021, 'Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics', Communications Biology, vol. 4, no. 1, 265. https://doi.org/10.1038/s42003-021-01797-9

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T1 - Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics

AU - Tsai, Chia Feng

AU - Zhang, Pengfei

AU - Scholten, David

AU - Martin, Kendall

AU - Wang, Yi Ting

AU - Zhao, Rui

AU - Chrisler, William B.

AU - Patel, Dhwani B.

AU - Dou, Maowei

AU - Jia, Yuzhi

AU - Reduzzi, Carolina

AU - Liu, Xia

AU - Moore, Ronald J.

AU - Burnum-Johnson, Kristin E.

AU - Lin, Miao Hsia

AU - Hsu, Chuan Chih

AU - Jacobs, Jon M.

AU - Kagan, Jacob

AU - Srivastava, Sudhir

AU - Rodland, Karin D.

AU - Steven Wiley, H.

AU - Qian, Wei Jun

AU - Smith, Richard D.

AU - Zhu, Ying

AU - Cristofanilli, Massimo

AU - Liu, Tao

AU - Liu, Huiping

AU - Shi, Tujin

PY - 2021/12

Y1 - 2021/12

N2 - Large numbers of cells are generally required for quantitative global proteome profiling due to surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible for rare cell populations (e.g., circulating tumor cells (CTCs)). Here we report a surfactant-assisted one-pot sample preparation coupled with mass spectrometry (MS) method termed SOP-MS for label-free global single-cell proteomics. SOP-MS capitalizes on the combination of a MS-compatible nonionic surfactant, n-Dodecyl-β-D-maltoside, and hydrophobic surface-based low-bind tubes or multi-well plates for ‘all-in-one’ one-pot sample preparation. This ‘all-in-one’ method including elimination of all sample transfer steps maximally reduces surface adsorption losses for effective processing of single cells, thus improving detection sensitivity for single-cell proteomics. This method allows convenient label-free quantification of hundreds of proteins from single human cells and ~1200 proteins from small tissue sections (close to ~20 cells). When applied to a patient CTC-derived xenograft (PCDX) model at the single-cell resolution, SOP-MS can reveal distinct protein signatures between primary tumor cells and early metastatic lung cells, which are related to the selection pressure of anti-tumor immunity during breast cancer metastasis. The approach paves the way for routine, precise, quantitative single-cell proteomics.

AB - Large numbers of cells are generally required for quantitative global proteome profiling due to surface adsorption losses associated with sample processing. Such bulk measurement obscures important cell-to-cell variability (cell heterogeneity) and makes proteomic profiling impossible for rare cell populations (e.g., circulating tumor cells (CTCs)). Here we report a surfactant-assisted one-pot sample preparation coupled with mass spectrometry (MS) method termed SOP-MS for label-free global single-cell proteomics. SOP-MS capitalizes on the combination of a MS-compatible nonionic surfactant, n-Dodecyl-β-D-maltoside, and hydrophobic surface-based low-bind tubes or multi-well plates for ‘all-in-one’ one-pot sample preparation. This ‘all-in-one’ method including elimination of all sample transfer steps maximally reduces surface adsorption losses for effective processing of single cells, thus improving detection sensitivity for single-cell proteomics. This method allows convenient label-free quantification of hundreds of proteins from single human cells and ~1200 proteins from small tissue sections (close to ~20 cells). When applied to a patient CTC-derived xenograft (PCDX) model at the single-cell resolution, SOP-MS can reveal distinct protein signatures between primary tumor cells and early metastatic lung cells, which are related to the selection pressure of anti-tumor immunity during breast cancer metastasis. The approach paves the way for routine, precise, quantitative single-cell proteomics.

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Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics

Abstract

Funding

ASJC Scopus subject areas

UN SDGs

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