IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-26514-2.html
   My bibliography  Save this article

High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Author

Listed:
  • Jongmin Woo

    (Pacific Northwest National Laboratory)

  • Sarah M. Williams

    (Pacific Northwest National Laboratory)

  • Lye Meng Markillie

    (Pacific Northwest National Laboratory)

  • Song Feng

    (Pacific Northwest National Laboratory)

  • Chia-Feng Tsai

    (Pacific Northwest National Laboratory)

  • Victor Aguilera-Vazquez

    (Pacific Northwest National Laboratory)

  • Ryan L. Sontag

    (Pacific Northwest National Laboratory)

  • Ronald J. Moore

    (Pacific Northwest National Laboratory)

  • Dehong Hu

    (Pacific Northwest National Laboratory)

  • Hardeep S. Mehta

    (Pacific Northwest National Laboratory)

  • Joshua Cantlon-Bruce

    (Scienion AG
    Cellenion SASU)

  • Tao Liu

    (Pacific Northwest National Laboratory)

  • Joshua N. Adkins

    (Pacific Northwest National Laboratory)

  • Richard D. Smith

    (Pacific Northwest National Laboratory)

  • Geremy C. Clair

    (Pacific Northwest National Laboratory)

  • Ljiljana Pasa-Tolic

    (Pacific Northwest National Laboratory)

  • Ying Zhu

    (Pacific Northwest National Laboratory)

Abstract

Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to 240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.

Suggested Citation

  • Jongmin Woo & Sarah M. Williams & Lye Meng Markillie & Song Feng & Chia-Feng Tsai & Victor Aguilera-Vazquez & Ryan L. Sontag & Ronald J. Moore & Dehong Hu & Hardeep S. Mehta & Joshua Cantlon-Bruce & T, 2021. "High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26514-2
    DOI: 10.1038/s41467-021-26514-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-26514-2
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-021-26514-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Ruedi Aebersold & Matthias Mann, 2016. "Mass-spectrometric exploration of proteome structure and function," Nature, Nature, vol. 537(7620), pages 347-355, September.
    2. Erwin M. Schoof & Benjamin Furtwängler & Nil Üresin & Nicolas Rapin & Simonas Savickas & Coline Gentil & Eric Lechman & Ulrich auf dem Keller & John E. Dick & Bo T. Porse, 2021. "Quantitative single-cell proteomics as a tool to characterize cellular hierarchies," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    3. Wenting Yang & Yuandong Tao & Yan Wu & Xinyuan Zhao & Weijie Ye & Dianyuan Zhao & Ling Fu & Caiping Tian & Jing Yang & Fuchu He & Li Tang, 2019. "Neutrophils promote the development of reparative macrophages mediated by ROS to orchestrate liver repair," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Yu Wang & Zhi-Ying Guan & Shao-Wen Shi & Yi-Rong Jiang & Jie Zhang & Yi Yang & Qiong Wu & Jie Wu & Jian-Bo Chen & Wei-Xin Ying & Qin-Qin Xu & Qian-Xi Fan & Hui-Feng Wang & Li Zhou & Ling Wang & Jin Fa, 2024. "Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Valdemaras Petrosius & Pedro Aragon-Fernandez & Nil Üresin & Gergo Kovacs & Teeradon Phlairaharn & Benjamin Furtwängler & Jeff Op De Beeck & Sarah L. Skovbakke & Steffen Goletz & Simon Francis Thomsen, 2023. "Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Claudia Ctortecka & Natalie M. Clark & Brian W. Boyle & Anjali Seth & D. R. Mani & Namrata D. Udeshi & Steven A. Carr, 2024. "Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Henry Webel & Lili Niu & Annelaura Bach Nielsen & Marie Locard-Paulet & Matthias Mann & Lars Juhl Jensen & Simon Rasmussen, 2024. "Imputation of label-free quantitative mass spectrometry-based proteomics data using self-supervised deep learning," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Yudong Gao & Daichi Shonai & Matthew Trn & Jieqing Zhao & Erik J. Soderblom & S. Alexandra Garcia-Moreno & Charles A. Gersbach & William C. Wetsel & Geraldine Dawson & Dmitry Velmeshev & Yong-hui Jian, 2024. "Proximity analysis of native proteomes reveals phenotypic modifiers in a mouse model of autism and related neurodevelopmental conditions," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    4. Sofani Tafesse Gebreyesus & Asad Ali Siyal & Reta Birhanu Kitata & Eric Sheng-Wen Chen & Bayarmaa Enkhbayar & Takashi Angata & Kuo-I Lin & Yu-Ju Chen & Hsiung-Lin Tu, 2022. "Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Kim Theilgaard-Mönch & Sachin Pundhir & Kristian Reckzeh & Jinyu Su & Marta Tapia & Benjamin Furtwängler & Johan Jendholm & Janus Schou Jakobsen & Marie Sigurd Hasemann & Kasper Jermiin Knudsen & Jack, 2022. "Transcription factor-driven coordination of cell cycle exit and lineage-specification in vivo during granulocytic differentiation," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Melih Yilmaz & William E. Fondrie & Wout Bittremieux & Carlo F. Melendez & Rowan Nelson & Varun Ananth & Sewoong Oh & William Stafford Noble, 2024. "Sequence-to-sequence translation from mass spectra to peptides with a transformer model," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Hao Hu & Wei Hu & An-Di Guo & Linhui Zhai & Song Ma & Hui-Jun Nie & Bin-Shan Zhou & Tianxian Liu & Xinglong Jia & Xing Liu & Xuebiao Yao & Minjia Tan & Xiao-Hua Chen, 2024. "Spatiotemporal and direct capturing global substrates of lysine-modifying enzymes in living cells," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    8. Christina Bligaard Pedersen & Søren Helweg Dam & Mike Bogetofte Barnkob & Michael D. Leipold & Noelia Purroy & Laura Z. Rassenti & Thomas J. Kipps & Jennifer Nguyen & James Arthur Lederer & Satyen Har, 2022. "cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    9. Yu Wang & Zhi-Ying Guan & Shao-Wen Shi & Yi-Rong Jiang & Jie Zhang & Yi Yang & Qiong Wu & Jie Wu & Jian-Bo Chen & Wei-Xin Ying & Qin-Qin Xu & Qian-Xi Fan & Hui-Feng Wang & Li Zhou & Ling Wang & Jin Fa, 2024. "Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    10. Yuwan Chen & Wen Zhou & Yufei Xia & Weijie Zhang & Qun Zhao & Xinwei Li & Hang Gao & Zhen Liang & Guanghui Ma & Kaiguang Yang & Lihua Zhang & Yukui Zhang, 2023. "Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    11. Martin Mehnert & Rodolfo Ciuffa & Fabian Frommelt & Federico Uliana & Audrey Drogen & Kilian Ruminski & Matthias Gstaiger & Ruedi Aebersold, 2020. "Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes," Nature Communications, Nature, vol. 11(1), pages 1-18, December.
    12. Daniela Klaproth-Andrade & Johannes Hingerl & Yanik Bruns & Nicholas H. Smith & Jakob Träuble & Mathias Wilhelm & Julien Gagneur, 2024. "Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    13. Erik Hartman & Aaron M. Scott & Christofer Karlsson & Tirthankar Mohanty & Suvi T. Vaara & Adam Linder & Lars Malmström & Johan Malmström, 2023. "Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    14. Fushi Wang & Chunxiao Zhao & Pinlong Zhao & Fanfan Chen & Dan Qiao & Jiandong Feng, 2023. "MoS2 nanopore identifies single amino acids with sub-1 Dalton resolution," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    15. Nicholas Drachman & Mathilde Lepoitevin & Hannah Szapary & Benjamin Wiener & William Maulbetsch & Derek Stein, 2024. "Nanopore ion sources deliver individual ions of amino acids and peptides directly into high vacuum," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    16. Simon Davis & Connor Scott & Janina Oetjen & Philip D. Charles & Benedikt M. Kessler & Olaf Ansorge & Roman Fischer, 2023. "Deep topographic proteomics of a human brain tumour," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    17. Wenping Zhou & Wenxue Li & Shisheng Wang & Barbora Salovska & Zhenyi Hu & Bo Tao & Yi Di & Ujwal Punyamurtula & Benjamin E. Turk & William C. Sessa & Yansheng Liu, 2023. "An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    18. Valdemaras Petrosius & Pedro Aragon-Fernandez & Nil Üresin & Gergo Kovacs & Teeradon Phlairaharn & Benjamin Furtwängler & Jeff Op De Beeck & Sarah L. Skovbakke & Steffen Goletz & Simon Francis Thomsen, 2023. "Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    19. Lu Li & Cuiji Sun & Yaoting Sun & Zhen Dong & Runxin Wu & Xiaoting Sun & Hanbin Zhang & Wenhao Jiang & Yan Zhou & Xufeng Cen & Shang Cai & Hongguang Xia & Yi Zhu & Tiannan Guo & Kiryl D. Piatkevich, 2022. "Spatially resolved proteomics via tissue expansion," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    20. Benjamin C. Orsburn & Yuting Yuan & Namandjé N. Bumpus, 2022. "Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26514-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.