Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

You’ve supercharged your research process with ACS and Mendeley!

STEP 1:
Click to create an ACS ID

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

MENDELEY PAIRING EXPIRED
Your Mendeley pairing has expired. Please reconnect
ACS Publications. Most Trusted. Most Cited. Most Read
Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform

OR SEARCH CITATIONS

My Activity
Publications

Figure 1Loading Img
Download Hi-Res ImageDownload to MS-PowerPointCite This:Anal. Chem. 2020, 92, 10, 7087-7095
    Article

    Sensitive Top-Down Proteomics Analysis of a Low Number of Mammalian Cells Using a Nanodroplet Sample Processing Platform
    Click to copy article linkArticle link copied!

    • Mowei Zhou
      Mowei Zhou
      Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
      More by Mowei Zhou
      Orcidhttp://orcid.org/0000-0003-3575-3224
    • Naomi Uwugiaren
      Naomi Uwugiaren
      International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
      More by Naomi Uwugiaren
    • Sarah M. Williams
      Sarah M. Williams
      Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
      More by Sarah M. Williams
    • Ronald J. Moore
      Ronald J. Moore
      Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
      More by Ronald J. Moore
      Orcidhttp://orcid.org/0000-0003-2806-2855
    • Rui Zhao
      Rui Zhao
      Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
      More by Rui Zhao
    • David Goodlett
      David Goodlett
      International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
      Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21201, United States
      More by David Goodlett
    • Irena Dapic
      Irena Dapic
      International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
      More by Irena Dapic
    • Ljiljana Paša-Tolić
      Ljiljana Paša-Tolić
      Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
      More by Ljiljana Paša-Tolić
    • Ying Zhu*
      Ying Zhu
      Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
      *[email protected]
      More by Ying Zhu
      Orcidhttp://orcid.org/0000-0002-5416-0566
    Other Access OptionsSupporting Information (2)

    Analytical Chemistry

    Cite this: Anal. Chem. 2020, 92, 10, 7087–7095
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.analchem.0c00467
    Published May 6, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    Top-down proteomics is a powerful tool for characterizing genetic variations and post-translational modifications at intact protein level. However, one significant technical gap of top-down proteomics is the inability to analyze a low amount of biological samples, which limits its access to isolated rare cells, fine needle aspiration biopsies, and tissue substructures. Herein, we developed an ultrasensitive top-down platform by incorporating a microfluidic sample preparation system, termed nanoPOTS (nanodroplet processing in one pot for trace samples), into a top-down proteomic workflow. A unique combination of a nonionic detergent dodecyl-β-d-maltopyranoside (DDM) with urea as protein extraction buffer significantly improved both protein extraction efficiency and sample recovery. We hypothesize that the DDM detergent improves protein recovery by efficiently reducing nonspecific adsorption of intact proteins on container surfaces, while urea serves as a strong denaturant to disrupt noncovalent complexes and release intact proteins for downstream analysis. The nanoPOTS-based top-down platform reproducibly and quantitatively identified ∼170 to ∼620 proteoforms from ∼70 to ∼770 HeLa cells containing ∼10 to ∼115 ng of total protein. A variety of post-translational modifications including acetylation, myristoylation, and iron binding were identified using only less than 800 cells. We anticipate the nanoPOTS top-down proteomics platform will be broadly applicable in biomedical research, particularly where clinical specimens are not available in amounts amenable to standard workflows.

    Copyright © 2020 American Chemical Society

    Subjects

    what are subjects

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    Supporting Information

    Click to copy section linkSection link copied!

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.analchem.0c00467.

    • Supporting data Figures S1–S9 (PDF)

    • Supporting data Tables S1–S5, with additional descriptions (XLSX)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    Click to copy section linkSection link copied!

    This article is cited by 38 publications.

    1. Ju Wang, Haiyan Tan, Yingxue Fu, Ashutosh Mishra, Huan Sun, Zhen Wang, Zhiping Wu, Xusheng Wang, Geidy E. Serrano, Thomas G. Beach, Junmin Peng, Anthony A. High. Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP. Journal of the American Society for Mass Spectrometry 2024, 35 (6) , 1253-1260. https://doi.org/10.1021/jasms.4c00067
    2. Zhitao Zhao, Yanting Guo, Trishika Chowdhury, Samin Anjum, Jiaxue Li, Lushuang Huang, Kellye A. Cupp-Sutton, Anthony Burgett, Dingjing Shi, Si Wu. Top-Down Proteomics Analysis of Picogram-Level Complex Samples Using Spray-Capillary-Based Capillary Electrophoresis–Mass Spectrometry. Analytical Chemistry 2024, 96 (21) , 8763-8771. https://doi.org/10.1021/acs.analchem.4c01119
    3. Evan A. Martin, James M. Fulcher, Mowei Zhou, Matthew E. Monroe, Vladislav A. Petyuk. TopPICR: A Companion R Package for Top-Down Proteomics Data Analysis. Journal of Proteome Research 2023, 22 (2) , 399-409. https://doi.org/10.1021/acs.jproteome.2c00570
    4. Kendall R. Johnson, Yunfan Gao, Michal Greguš, Alexander R. Ivanov. On-capillary Cell Lysis Enables Top-down Proteomic Analysis of Single Mammalian Cells by CE-MS/MS. Analytical Chemistry 2022, 94 (41) , 14358-14367. https://doi.org/10.1021/acs.analchem.2c03045
    5. Kevin J. Zemaitis, Dušan Veličković, William Kew, Kyle L. Fort, Maria Reinhardt-Szyba, Annapurna Pamreddy, Yanli Ding, Dharam Kaushik, Kumar Sharma, Alexander A. Makarov, Mowei Zhou, Ljiljana Paša-Tolić. Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection. Analytical Chemistry 2022, 94 (37) , 12604-12613. https://doi.org/10.1021/acs.analchem.2c01034
    6. Philipp T. Kaulich, Liam Cassidy, Konrad Winkels, Andreas Tholey. Improved Identification of Proteoforms in Top-Down Proteomics Using FAIMS with Internal CV Stepping. Analytical Chemistry 2022, 94 (8) , 3600-3607. https://doi.org/10.1021/acs.analchem.1c05123
    7. Sara Kassem, Kyra van der Pan, Anniek L. de Jager, Brigitta A. E. Naber, Inge F. de Laat, Alesha Louis, Jacques J. M. van Dongen, Cristina Teodosio, Paula Díez. Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis. Journal of Proteome Research 2021, 20 (9) , 4217-4230. https://doi.org/10.1021/acs.jproteome.1c00321
    8. Kenneth Weke, Ashita Singh, Naomi Uwugiaren, Javier A. Alfaro, Tongjie Wang, Ted R. Hupp, J. Robert O’Neill, Borek Vojtesek, David R. Goodlett, Sarah M. Williams, Mowei Zhou, Ryan T. Kelly, Ying Zhu, Irena Dapic. MicroPOTS Analysis of Barrett’s Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress. Journal of Proteome Research 2021, 20 (5) , 2195-2205. https://doi.org/10.1021/acs.jproteome.0c00629
    9. Benoit Gilquin, Myriam Cubizolles, Remco Den Dulk, Frédéric Revol-Cavalier, Manuel Alessio, Charles-Elie Goujon, Camille Echampard, Gorka Arrizabalaga, Annie Adrait, Mathilde Louwagie, Patricia Laurent, Fabrice P. Navarro, Yohann Couté, Marie-Line Cosnier, Virginie Brun. PepS: An Innovative Microfluidic Device for Bedside Whole Blood Processing before Plasma Proteomics Analyses. Analytical Chemistry 2021, 93 (2) , 683-690. https://doi.org/10.1021/acs.analchem.0c02270
    10. Matthew Waas, Thomas Kislinger. Addressing Cellular Heterogeneity in Cancer through Precision Proteomics. Journal of Proteome Research 2020, 19 (9) , 3607-3619. https://doi.org/10.1021/acs.jproteome.0c00338
    11. David S. Roberts, Joseph A. Loo, Yury O. Tsybin, Xiaowen Liu, Si Wu, Julia Chamot-Rooke, Jeffrey N. Agar, Ljiljana Paša-Tolić, Lloyd M. Smith, Ying Ge. Top-down proteomics. Nature Reviews Methods Primers 2024, 4 (1) https://doi.org/10.1038/s43586-024-00318-2
    12. Tanushree Dutta, Julea Vlassakis. Microscale measurements of protein complexes from single cells. Current Opinion in Structural Biology 2024, 87 , 102860. https://doi.org/10.1016/j.sbi.2024.102860
    13. Tian Xu, Qianjie Wang, Qianyi Wang, Liangliang Sun. Mass spectrometry-intensive top-down proteomics: an update on technology advancements and biomedical applications. Analytical Methods 2024, 16 (28) , 4664-4682. https://doi.org/10.1039/D4AY00651H
    14. Yong Chiang Tan, Teck Yew Low, Pey Yee Lee, Lay Cheng Lim. Single‐cell proteomics by mass spectrometry: Advances and implications in cancer research. PROTEOMICS 2024, 24 (12-13) https://doi.org/10.1002/pmic.202300210
    15. Kyowon Jeong, Philipp T. Kaulich, Wonhyeuk Jung, Jihyung Kim, Andreas Tholey, Oliver Kohlbacher. Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top‐down proteomics. PROTEOMICS 2024, 24 (3-4) https://doi.org/10.1002/pmic.202300068
    16. Shweta Jain, Pushpendra Kumar, Mudit Kumar, Ankur Vaidya. Analytical methods in the detection of proteins and peptides in tissue fluids and homogenates. 2024, 235-259. https://doi.org/10.1016/B978-0-443-18925-8.00009-X
    17. Leena R. Pade, Kaitlyn E. Stepler, Erika P. Portero, Kellen DeLaney, Peter Nemes. Biological mass spectrometry enables spatiotemporal ‘omics: From tissues to cells to organelles. Mass Spectrometry Reviews 2024, 43 (1) , 106-138. https://doi.org/10.1002/mas.21824
    18. John P. McGee, Pei Su, Kenneth R. Durbin, Michael A. R. Hollas, Nicholas W. Bateman, G. Larry Maxwell, Thomas P. Conrads, Ryan T. Fellers, Rafael D. Melani, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher. Automated imaging and identification of proteoforms directly from ovarian cancer tissue. Nature Communications 2023, 14 (1) https://doi.org/10.1038/s41467-023-42208-3
    19. Ketki Bagwe, Noah Gould, Kendall R. Johnson, Alexander R. Ivanov. Single-cell omic molecular profiling using capillary electrophoresis-mass spectrometry. TrAC Trends in Analytical Chemistry 2023, 165 , 117117. https://doi.org/10.1016/j.trac.2023.117117
    20. Jan Leipert, Philipp T. Kaulich, Max K. Steinbach, Britta Steer, Konrad Winkels, Christine Blurton, Matthias Leippe, Andreas Tholey. Elution von intakten Proteoformen von magnetischen Partikeln kombiniert mit digitaler Mikrofluidik für die quantitative Top‐down‐Nanoproteomik von einzelnen C. elegans ‐Nematoden. Angewandte Chemie 2023, 135 (28) https://doi.org/10.1002/ange.202301969
    21. Jan Leipert, Philipp T. Kaulich, Max K. Steinbach, Britta Steer, Konrad Winkels, Christine Blurton, Matthias Leippe, Andreas Tholey. Digital Microfluidics and Magnetic Bead‐Based Intact Proteoform Elution for Quantitative Top‐down Nanoproteomics of Single C. elegans Nematodes. Angewandte Chemie International Edition 2023, 62 (28) https://doi.org/10.1002/anie.202301969
    22. Sydney Sunna, Christine A. Bowen, Christina C. Ramelow, Juliet V. Santiago, Prateek Kumar, Srikant Rangaraju. Advances in proteomic phenotyping of microglia in neurodegeneration. PROTEOMICS 2023, 23 (13-14) https://doi.org/10.1002/pmic.202200183
    23. Jessica L. Nickerson, Venus Baghalabadi, Subin R. C. K. Rajendran, Philip J. Jakubec, Hammam Said, Teresa S. McMillen, Ziheng Dang, Alan A. Doucette. Recent advances in top‐down proteome sample processing ahead of MS analysis. Mass Spectrometry Reviews 2023, 42 (2) , 457-495. https://doi.org/10.1002/mas.21706
    24. Yen-Chen Liao, James M. Fulcher, David J. Degnan, Sarah M. Williams, Lisa M. Bramer, Dušan Veličković, Kevin J. Zemaitis, Marija Veličković, Ryan L. Sontag, Ronald J. Moore, Ljiljana Paša-Tolić, Ying Zhu, Mowei Zhou. Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform. Molecular & Cellular Proteomics 2023, 22 (2) , 100491. https://doi.org/10.1016/j.mcpro.2022.100491
    25. Anca-Narcisa Neagu, Madhuri Jayathirtha, Danielle Whitham, Panashe Mutsengi, Isabelle Sullivan, Brindusa Alina Petre, Costel C. Darie. Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022, 10 (4) , 35. https://doi.org/10.3390/proteomes10040035
    26. Yumi Kwon, Paul D. Piehowski, Rui Zhao, Ryan L. Sontag, Ronald J. Moore, Kristin E. Burnum-Johnson, Richard D. Smith, Wei-Jun Qian, Ryan T. Kelly, Ying Zhu. Hanging drop sample preparation improves sensitivity of spatial proteomics. Lab on a Chip 2022, 22 (15) , 2869-2877. https://doi.org/10.1039/D2LC00384H
    27. Manxi Yang, Hang Hu, Pei Su, Paul M. Thomas, Jeannie M. Camarillo, Joseph B. Greer, Bryan P. Early, Ryan T. Fellers, Neil L. Kelleher, Julia Laskin. Proteoform‐Selective Imaging of Tissues Using Mass Spectrometry**. Angewandte Chemie 2022, 134 (29) https://doi.org/10.1002/ange.202200721
    28. Manxi Yang, Hang Hu, Pei Su, Paul M. Thomas, Jeannie M. Camarillo, Joseph B. Greer, Bryan P. Early, Ryan T. Fellers, Neil L. Kelleher, Julia Laskin. Proteoform‐Selective Imaging of Tissues Using Mass Spectrometry**. Angewandte Chemie International Edition 2022, 61 (29) https://doi.org/10.1002/anie.202200721
    29. Anca-Narcisa Neagu, Madhuri Jayathirtha, Emma Baxter, Mary Donnelly, Brindusa Alina Petre, Costel C. Darie. Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules 2022, 27 (8) , 2411. https://doi.org/10.3390/molecules27082411
    30. Rachele A. Lubeckyj, Liangliang Sun. Laser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain. Molecular Omics 2022, 18 (2) , 112-122. https://doi.org/10.1039/D1MO00335F
    31. Michael A R Hollas, Matthew T Robey, Ryan T Fellers, Richard D LeDuc, Paul M Thomas, Neil L Kelleher. The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms. Nucleic Acids Research 2022, 50 (D1) , D526-D533. https://doi.org/10.1093/nar/gkab1086
    32. Yingyan Zhou, Guangsheng Guo, Xiayan Wang. Development of Ultranarrow‐Bore Open Tubular High Efficiency Liquid Chromatography. Chinese Journal of Chemistry 2022, 40 (1) , 137-152. https://doi.org/10.1002/cjoc.202100445
    33. Michal Alexovič, Ján Sabo, Rémi Longuespée. Automation of single‐cell proteomic sample preparation. PROTEOMICS 2021, 21 (23-24) https://doi.org/10.1002/pmic.202100198
    34. Julea Vlassakis, Louise L. Hansen, Ryo Higuchi-Sanabria, Yun Zhou, C. Kimberly Tsui, Andrew Dillin, Haiyan Huang, Amy E. Herr. Measuring expression heterogeneity of single-cell cytoskeletal protein complexes. Nature Communications 2021, 12 (1) https://doi.org/10.1038/s41467-021-25212-3
    35. Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Paša-Tolić, Yury O. Tsybin, Neil L. Kelleher, . The Human Proteoform Project: Defining the human proteome. Science Advances 2021, 7 (46) https://doi.org/10.1126/sciadv.abk0734
    36. Michal Alexovič, Ján Sabo, Rémi Longuespée. Microproteomic sample preparation. PROTEOMICS 2021, 21 (9) https://doi.org/10.1002/pmic.202000318
    37. Zhichang Yang, Liangliang Sun. Recent technical progress in sample preparation and liquid-phase separation-mass spectrometry for proteomic analysis of mass-limited samples. Analytical Methods 2021, 13 (10) , 1214-1225. https://doi.org/10.1039/D1AY00171J
    38. Kyle A. Brown, Jake A. Melby, David S. Roberts, Ying Ge. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Review of Proteomics 2020, 17 (10) , 719-733. https://doi.org/10.1080/14789450.2020.1855982
    Download PDF
    Go to Analytical Chemistry
    Get e-Alerts
    Get e-Alerts

    Analytical Chemistry

    Cite this: Anal. Chem. 2020, 92, 10, 7087–7095
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.analchem.0c00467
    Published May 6, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

    Article Views

    2420

    Altmetric

    -

    Citations

    38
    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.