IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-49651-w.html
   My bibliography  Save this article

Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications

Author

Listed:
  • Claudia Ctortecka

    (Broad Institute of MIT and Harvard)

  • Natalie M. Clark

    (Broad Institute of MIT and Harvard)

  • Brian W. Boyle

    (Broad Institute of MIT and Harvard)

  • Anjali Seth

    (Cellenion SASU)

  • D. R. Mani

    (Broad Institute of MIT and Harvard)

  • Namrata D. Udeshi

    (Broad Institute of MIT and Harvard)

  • Steven A. Carr

    (Broad Institute of MIT and Harvard)

Abstract

The recent technological and computational advances in mass spectrometry-based single-cell proteomics have pushed the boundaries of sensitivity and throughput. However, reproducible quantification of thousands of proteins within a single cell remains challenging. To address some of those limitations, we present a dedicated sample preparation chip, the proteoCHIP EVO 96 that directly interfaces with the Evosep One. This, in combination with the Bruker timsTOF demonstrates double the identifications without manual sample handling and the newest generation timsTOF Ultra identifies up to 4000 with an average of 3500 protein groups per single HEK-293T without a carrier or match-between runs. Our workflow spans 4 orders of magnitude, identifies over 50 E3 ubiquitin-protein ligases, and profiles key regulatory proteins upon small molecule stimulation. This study demonstrates that the proteoCHIP EVO 96-based sample preparation with the timsTOF Ultra provides sufficient proteome depth to study complex biology beyond cell-type classifications.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49651-w
    DOI: 10.1038/s41467-024-49651-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-49651-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-024-49651-w?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. Orit Rozenblatt-Rosen & Michael J. T. Stubbington & Aviv Regev & Sarah A. Teichmann, 2017. "The Human Cell Atlas: from vision to reality," Nature, Nature, vol. 550(7677), pages 451-453, October.
    2. Ruedi Aebersold & Matthias Mann, 2016. "Mass-spectrometric exploration of proteome structure and function," Nature, Nature, vol. 537(7620), pages 347-355, September.
    3. Zilu Ye & Pierre Sabatier & Javier Martin-Gonzalez & Akihiro Eguchi & Maico Lechner & Ole Østergaard & Jingsheng Xie & Yuan Guo & Lesley Schultz & Rafaela Truffer & Dorte B. Bekker-Jensen & Nicolai Ba, 2024. "One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    4. 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.
    5. 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.
    6. Sarah Djebali & Carrie A. Davis & Angelika Merkel & Alex Dobin & Timo Lassmann & Ali Mortazavi & Andrea Tanzer & Julien Lagarde & Wei Lin & Felix Schlesinger & Chenghai Xue & Georgi K. Marinov & Jaina, 2012. "Landscape of transcription in human cells," Nature, Nature, vol. 489(7414), pages 101-108, September.
    Full references (including those not matched with items on IDEAS)

    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. 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.
    2. 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.
    3. 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.
    4. Manuel Matzinger & Anna Schmücker & Ramesh Yelagandula & Karel Stejskal & Gabriela Krššáková & Frédéric Berger & Karl Mechtler & Rupert L. Mayer, 2024. "Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    5. Christoph Ziegenhain & Rickard Sandberg, 2021. "BAMboozle removes genetic variation from human sequence data for open data sharing," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    6. Katharina T. Schmid & Barbara Höllbacher & Cristiana Cruceanu & Anika Böttcher & Heiko Lickert & Elisabeth B. Binder & Fabian J. Theis & Matthias Heinig, 2021. "scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies," Nature Communications, Nature, vol. 12(1), pages 1-18, December.
    7. 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.
    8. 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.
    9. Letizia Pitto & Francesca Gorini & Fabrizio Bianchi & Elena Guzzolino, 2020. "New Insights into Mechanisms of Endocrine-Disrupting Chemicals in Thyroid Diseases: The Epigenetic Way," IJERPH, MDPI, vol. 17(21), pages 1-18, October.
    10. Edie-Rosmin Wu & Ming-Ju Hsieh & Whei-Ling Chiang & Kuan-Chun Hsueh & Shun-Fa Yang & Shih-Chi Su, 2019. "Association of lncRNA CCAT2 and CASC8 Gene Polymorphisms with Hepatocellular Carcinoma," IJERPH, MDPI, vol. 16(16), pages 1-11, August.
    11. Aiko Sekita & Hiroshi Kawasaki & Ayano Fukushima-Nomura & Kiyoshi Yashiro & Keiji Tanese & Susumu Toshima & Koichi Ashizaki & Tomohiro Miyai & Junshi Yazaki & Atsuo Kobayashi & Shinichi Namba & Tatsuh, 2023. "Multifaceted analysis of cross-tissue transcriptomes reveals phenotype–endotype associations in atopic dermatitis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    12. Zhantao Shao & Jack Hu & Allison Jandura & Ronit Wilk & Matthew Jachimowicz & Lingfeng Ma & Chun Hu & Abby Sundquist & Indrani Das & Phillip Samuel-Larbi & Julie A. Brill & Henry M. Krause, 2024. "Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    13. Anne-Emmanuelle Foucher & Leila Touat-Todeschini & Ariadna B. Juarez-Martinez & Auriane Rakitch & Hamida Laroussi & Claire Karczewski & Samira Acajjaoui & Montserrat Soler-López & Stephen Cusack & Cam, 2022. "Structural analysis of Red1 as a conserved scaffold of the RNA-targeting MTREC/PAXT complex," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    14. Ajita Shree & Musale Krushna Pavan & Hamim Zafar, 2023. "scDREAMER for atlas-level integration of single-cell datasets using deep generative model paired with adversarial classifier," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    15. Yingxin Lin & Yue Cao & Elijah Willie & Ellis Patrick & Jean Y. H. Yang, 2023. "Atlas-scale single-cell multi-sample multi-condition data integration using scMerge2," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    16. 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.
    17. 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.
    18. Anna Cioce & Beatriz Calle & Tatiana Rizou & Sarah C. Lowery & Victoria L. Bridgeman & Keira E. Mahoney & Andrea Marchesi & Ganka Bineva-Todd & Helen Flynn & Zhen Li & Omur Y. Tastan & Chloe Roustan &, 2022. "Cell-specific bioorthogonal tagging of glycoproteins," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    19. Yi Yang & Qun Fang, 2024. "Prediction of glycopeptide fragment mass spectra by deep learning," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    20. 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.

    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:15:y:2024:i:1:d:10.1038_s41467-024-49651-w. 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.