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Spectroscape enables real-time query and visualization of a spectral archive in proteomics

Author

Listed:
  • Long Wu

    (The Hong Kong University of Science and Technology
    The Hong Kong University of Science and Technology)

  • Ayman Hoque

    (The Hong Kong University of Science and Technology)

  • Henry Lam

    (The Hong Kong University of Science and Technology)

Abstract

In proteomics, spectral archives organize the enormous amounts of publicly available peptide tandem mass spectra by similarity, offering opportunities for error correction and novel discoveries. Here we adapt an indexing algorithm developed by Facebook for organizing online multimedia resources to tandem mass spectra and achieve practically instantaneous retrieval and clustering of approximate nearest neighbors in a large spectral archive. An interactive web-based graphical user interface enables the user to view a query spectrum in its clustered neighborhood, which facilitates contextual validation of peptide identifications and exploration of the dark proteome.

Suggested Citation

  • Long Wu & Ayman Hoque & Henry Lam, 2023. "Spectroscape enables real-time query and visualization of a spectral archive in proteomics," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42006-x
    DOI: 10.1038/s41467-023-42006-x
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    References listed on IDEAS

    as
    1. Min-Sik Kim & Sneha M. Pinto & Derese Getnet & Raja Sekhar Nirujogi & Srikanth S. Manda & Raghothama Chaerkady & Anil K. Madugundu & Dhanashree S. Kelkar & Ruth Isserlin & Shobhit Jain & Joji K. Thoma, 2014. "A draft map of the human proteome," Nature, Nature, vol. 509(7502), pages 575-581, May.
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