ArticleNature biotechnology2022
Deep Visual Proteomics defines single-cell identity and heterogeneity.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 332 papers, 2 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
332 citing papers in PubMed, 2 syntheses or guidelines pooled it, 487 citations in OpenAlex.
- Mass spectrometry-based human spatial omics: fundamentals, innovations, and applications.Journal of biomedical science · 2026Pooled it
- Progress and trends on machine learning in proteomics during 1997-2024: a bibliometric analysis.Frontiers in medicine · 2025Pooled it
- A modular framework for antibody-drug conjugate biomarkers.Nature reviews. Clinical oncology · 2026Review
- Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Spatial Proteomics as a Potential Decision-Support Layer for Early Melanoma: A Narrative Review.International journal of dermatology · 2026Review
- Emerging technologies in the spatial proteomics landscape.Analytical and bioanalytical chemistry · 2026Review
- Review
- Article
- A spatial and temporal transcriptomic atlas of mouse intestinal regeneration in the jejunum.Nature communications · 2026Article
- Targeting GLUTs in Cancer: Mechanisms, Combination Strategies, and Translational Challenges.Current medical science · 2026Review
- Pushing the limits of single-cell proteomics to investigate bacterial heterogeneity using bacSCP.Nature communications · 2026Article
- Senotypes define the diverse landscape of senescent cells.Nature aging · 2026Review
- Deep visual multi-omics profiling links morphology and molecular programs in clear cell renal cell carcinoma.EMBO molecular medicine · 2026Article
- Post-translational modification of proteins in the human testis development pathway.Human reproduction update · 2026Review
- MultiSpaceNet: graph-based joint representation learning for paired spatial transcriptome-proteome data.Bioinformatics (Oxford, England) · 2026Article
- A reference protein atlas of the adult mouse brain vasculature.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Spatial Immune Coding in Tumor-Draining Lymph Nodes: Functional Compartmentalization of Immune Activation and Immunosuppression.International journal of molecular sciences · 2026Review
- Single Cell-Type Spatial Proteomics Uncovers Regional Heterogeneity of Astrocytes.Journal of proteome research · 2026Article
- Cardiac immunity and heart repair: Mechanism, challenge, and future direction.Chinese medical journal · 2026Review
272 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
21 authors at 7 institutions in 7 countries.
Funding
Abstract
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.