Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells

Martin, Kendall D.; Zhang, Tong; Lin, Tai-Tu; Habowski, Amber N.; Zhao, Rui; Tsai, Chia-Feng; Chrisler, William B.; Sontag, Ryan L.; Orton, Daniel J.; Lu, Yong-Jie; Rodland, Karin D.; Yang, Bin; Liu, Tao; Smith, Richard D.; Qian, Weijun; Waterman, Marian L.; Wiley, H Steven; Shi, Tujin

doi:10.1021/acs.jproteome.1c00403

Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells

Journal Article · Thu Aug 05 00:00:00 EDT 2021 · Journal of Proteome Research

DOI:https://doi.org/10.1021/acs.jproteome.1c00403· OSTI ID:1837663

Martin, Kendall D. ^[1]; Zhang, Tong ^[2]; Lin, Tai-Tu ^[2]; Habowski, Amber N. ^[3]; Zhao, Rui ^[2]; Tsai, Chia-Feng ^[2]; Chrisler, William B. ^[2]; Sontag, Ryan L. ^[2]; ^[2]; Lu, Yong-Jie ^[3]; ^[2]; Yang, Bin ^[1]; ^[2]; ^[2]; ^[2]; Waterman, Marian L. ^[3]; ^[2]; Shi, Tujin ^[2]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Washington State Univ., Richland, WA (United States)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Univ. of California, Irvine, CA (United States)

Recent advances in sample preparation enable label-free MS-based proteome profiling of small numbers of mammalian cells. However, specific devices are often required to downscale sample processing volume from the standard 50-200 µL to sub-µL for effective nanoproteomics, which greatly impedes the implementation of current nanoproteomics methods by broad proteomics research community. Here we report a facile one-pot nanoproteomics method termed SOPs-MS (Surfactant-assisted One-Pot sample processing at the standard volume coupled with MS) for convenient proteome profiling of 50-1000 mammalian cells. Building upon our recent development of SOP-MS for label-free single-cell proteomics at low µL volume (Commun Bio 2021, 4, 265), we have systematically evaluated its processing volume at 10-200 µL using 100 human cells for robust reproducible nanoproteomic analysis. The processing volume of 50 µL which is in the range of volume for standard proteomics sample preparation, has been selected for easy sample handling with benchtop micropipette. Using the commonly accessible LC-MS platform, SOPs-MS allows for reliable label-free quantification of ~1200-2700 protein groups from 50-1000 MCF10A cells. When applied to small subpopulations of mouse colon crypt cells, SOPs-MS can reveal distinct protein signatures between any two subpopulation cells with identification of ~1500-2500 protein groups for each subpopulation. SOPs-MS may pave the way for routine deep proteome profiling of small numbers of cells as well as low-input samples.

View Accepted Manuscript (DOE)

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-76RL01830

OSTI ID:: 1837663

Report Number(s):: PNNL-SA--160823

Journal Information:: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 9 Vol. 20; ISSN 1535-3893

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

References (38)

Benchtop-compatible sample processing workflow for proteome profiling of < 100 mammalian cells Xu, Kerui; Liang, Yiran; Piehowski, Paul D. Analytical and Bioanalytical Chemistry, Vol. 411, Issue 19 https://doi.org/10.1007/s00216-018-1493-9	journal	November 2018
Cellular Heterogeneity: Do Differences Make a Difference? Altschuler, Steven J.; Wu, Lani F. Cell, Vol. 141, Issue 4 https://doi.org/10.1016/j.cell.2010.04.033	journal	May 2010
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer Zhang, Hui; Liu, Tao; Zhang, Zhen Cell, Vol. 166, Issue 3 https://doi.org/10.1016/j.cell.2016.05.069	journal	July 2016
Redefining Signaling Pathways with an Expanding Single-Cell Toolbox Gaudet, Suzanne; Miller-Jensen, Kathryn Trends in Biotechnology, Vol. 34, Issue 6 https://doi.org/10.1016/j.tibtech.2016.02.009	journal	June 2016
Single-Cell Multiomics: Multiple Measurements from Single Cells Macaulay, Iain C.; Ponting, Chris P.; Voet, Thierry Trends in Genetics, Vol. 33, Issue 2 https://doi.org/10.1016/j.tig.2016.12.003	journal	February 2017
Achieving 50% Ionization Efficiency in Subambient Pressure Ionization with Nanoelectrospray Marginean, Ioan; Page, Jason S.; Tolmachev, Aleksey V. Analytical Chemistry, Vol. 82, Issue 22 https://doi.org/10.1021/ac1019123	journal	November 2010
Miniaturized Filter-Aided Sample Preparation (MICRO-FASP) Method for High Throughput, Ultrasensitive Proteomics Sample Preparation Reveals Proteome Asymmetry in Xenopus laevis Embryos Zhang, Zhenbin; Dubiak, Kyle M.; Huber, Paul W. Analytical Chemistry, Vol. 92, Issue 7 https://doi.org/10.1021/acs.analchem.0c00470	journal	March 2020
Improved Sensitivity of Ultralow Flow LC–MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology Greguš, Michal; Kostas, James C.; Ray, Somak Analytical Chemistry, Vol. 92, Issue 21 https://doi.org/10.1021/acs.analchem.0c03262	journal	October 2020
Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling Liang, Yiran; Acor, Hayden; McCown, Michaela A. Analytical Chemistry, Vol. 93, Issue 3 https://doi.org/10.1021/acs.analchem.0c04240	journal	December 2020
Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis Li, Zi-Yi; Huang, Min; Wang, Xiu-Kun Analytical Chemistry, Vol. 90, Issue 8 https://doi.org/10.1021/acs.analchem.8b00661	journal	March 2018
Comprehensive Single-Shot Proteomics with FAIMS on a Hybrid Orbitrap Mass Spectrometer Hebert, Alexander S.; Prasad, Satendra; Belford, Michael W. Analytical Chemistry, Vol. 90, Issue 15 https://doi.org/10.1021/acs.analchem.8b02233	journal	July 2018
Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling Shao, Xi; Wang, Xuantang; Guan, Sheng Analytical Chemistry, Vol. 90, Issue 23 https://doi.org/10.1021/acs.analchem.8b03692	journal	October 2018
Carrier-Assisted Single-Tube Processing Approach for Targeted Proteomics Analysis of Low Numbers of Mammalian Cells Zhang, Pengfei; Gaffrey, Matthew J.; Zhu, Ying Analytical Chemistry, Vol. 91, Issue 2 https://doi.org/10.1021/acs.analchem.8b04258	journal	November 2018
Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells Yi, Lian; Tsai, Chia-Feng; Dirice, Ercument Analytical Chemistry, Vol. 91, Issue 9 https://doi.org/10.1021/acs.analchem.9b00024	journal	March 2019
Step-Wise Assessment and Optimization of Sample Handling Recovery Yield for Nanoproteomic Analysis of 1000 Mammalian Cells Wu, Ruilin; Xing, Sansi; Badv, Maryam Analytical Chemistry, Vol. 91, Issue 16 https://doi.org/10.1021/acs.analchem.9b02092	journal	July 2019
High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labeling in a Nanodroplet Sample Preparation Platform Dou, Maowei; Clair, Geremy; Tsai, Chia-Feng Analytical Chemistry, Vol. 91, Issue 20 https://doi.org/10.1021/acs.analchem.9b03349	journal	September 2019
In-Line Sample Processing System with an Immobilized Trypsin-Packed Fused-Silica Capillary Tube for the Proteomic Analysis of a Small Number of Mammalian Cells Hata, Kosuke; Izumi, Yoshihiro; Hara, Takeshi Analytical Chemistry, Vol. 92, Issue 4 https://doi.org/10.1021/acs.analchem.9b03993	journal	January 2020
National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions Kagan, Jacob; Moritz, Robert L.; Mazurchuk, Richard Journal of Proteome Research, Vol. 19, Issue 5 https://doi.org/10.1021/acs.jproteome.0c00021	journal	March 2020
MPK4 Phosphorylation Dynamics and Interacting Proteins in Plant Immunity Zhang, Tong; Schneider, Jacqueline D.; Lin, Chuwei Journal of Proteome Research, Vol. 18, Issue 3 https://doi.org/10.1021/acs.jproteome.8b00345	journal	January 2019
Mass spectrometry-based proteomics Aebersold, Ruedi; Mann, Matthias Nature, Vol. 422, Issue 6928 https://doi.org/10.1038/nature01511	journal	March 2003
Proteogenomic characterization of human colon and rectal cancer Zhang, Bing; Wang, Jing; Wang, Xiaojing Nature, Vol. 513, Issue 7518 https://doi.org/10.1038/nature13438	journal	July 2014
Proteogenomics connects somatic mutations to signalling in breast cancer Mertins, Philipp; Mani, D. R.; Ruggles, Kelly V. Nature, Vol. 534, Issue 7605 https://doi.org/10.1038/nature18003	journal	May 2016
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Cox, Jürgen; Mann, Matthias Nature Biotechnology, Vol. 26, Issue 12 https://doi.org/10.1038/nbt.1511	journal	November 2008
Universal sample preparation method for proteome analysis Wiśniewski, Jacek R.; Zougman, Alexandre; Nagaraj, Nagarjuna Nature Methods, Vol. 6, Issue 5 https://doi.org/10.1038/nmeth.1322	journal	April 2009
Single-cell western blotting Hughes, Alex J.; Spelke, Dawn P.; Xu, Zhuchen Nature Methods, Vol. 11, Issue 7 https://doi.org/10.1038/nmeth.2992	journal	June 2014
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics Kong, Andy T.; Leprevost, Felipe V.; Avtonomov, Dmitry M. Nature Methods, Vol. 14, Issue 5 https://doi.org/10.1038/nmeth.4256	journal	April 2017
Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells Zhu, Ying; Piehowski, Paul D.; Zhao, Rui Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-03367-w	journal	February 2018
Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells Shi, Tujin; Gaffrey, Matthew J.; Fillmore, Thomas L. Communications Biology, Vol. 1, Issue 1 https://doi.org/10.1038/s42003-018-0107-6	journal	August 2018
Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt Habowski, Amber N.; Flesher, Jessica L.; Bates, Jennifer M. Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-01181-z	journal	August 2020
Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics Tsai, Chia-Feng; Zhang, Pengfei; Scholten, David Communications Biology, Vol. 4, Issue 1 https://doi.org/10.1038/s42003-021-01797-9	journal	March 2021
New frontiers for mass spectrometry based upon structures for lossless ion manipulations Ibrahim, Yehia M.; Hamid, Ahmed M.; Deng, Liulin The Analyst, Vol. 142, Issue 7 https://doi.org/10.1039/c7an00031f	journal	January 2017
An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics Tsai, Chia-Feng; Zhao, Rui; Williams, Sarah M. Molecular & Cellular Proteomics, Vol. 19, Issue 5 https://doi.org/10.1074/mcp.ra119.001857	journal	May 2020
jPOSTrepo: an international standard data repository for proteomes Okuda, Shujiro; Watanabe, Yu; Moriya, Yuki Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1080	journal	November 2016
Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway Shi, Tujin; Niepel, Mario; McDermott, Jason E. Science Signaling, Vol. 9, Issue 436 https://doi.org/10.1126/scisignal.aaf0891	journal	July 2016
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation Budnik, Bogdan; Levy, Ezra; Harmange, Guillaume Genome Biology, Vol. 19, Issue 1 https://doi.org/10.1186/s13059-018-1547-5	journal	October 2018
Hallmarks of intestinal stem cells Baulies, Anna; Angelis, Nikolaos; Li, Vivian S. W. Development, Vol. 147, Issue 15 https://doi.org/10.1242/dev.182675	journal	August 2020
Automated sample preparation with SP 3 for low‐input clinical proteomics Müller, Torsten; Kalxdorf, Mathias; Longuespée, Rémi Molecular Systems Biology, Vol. 16, Issue 1 https://doi.org/10.15252/msb.20199111	journal	January 2020
Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells Martin, Kendall; Zhang, Tong; Zhang, Pengfei Journal of Visualized Experiments, Issue 165 https://doi.org/10.3791/61797	journal	January 2020

Similar Records

Robust surfactant-assisted one-pot sample preparation for label-free single-cell and nanoscale proteomics

Book · Sat Jun 22 00:00:00 EDT 2024 · OSTI ID:2477155

Nanoproteomics Comes of Age

Journal Article · Thu Nov 01 00:00:00 EDT 2018 · Expert Review of Proteomics · OSTI ID:1582608

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

Journal Article · Sun Feb 28 19:00:00 EST 2021 · Communications Biology · OSTI ID:1783692

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Cells
Mass spectrometry
Peptides and proteins
Protein identification
Proteomics
SOPs-MS
colon crypt cells
nanoproteomics
small numbers of cells
surfactant DDM

Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50–1000 Mammalian Cells

Citation Formats

References (38)

Similar Records

Related Subjects