Spectroscape enables real-time query and visualization of a spectral archive in proteomics
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 resou...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-10-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-42006-x |
| _version_ | 1797558659652255744 |
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| author | Long Wu Ayman Hoque Henry Lam |
| author_facet | Long Wu Ayman Hoque Henry Lam |
| author_sort | Long Wu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T17:34:23Z |
| format | Article |
| id | doaj.art-704d880e717247e79419ba738e2a3751 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-10T17:34:23Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-704d880e717247e79419ba738e2a37512023-11-20T09:54:26ZengNature PortfolioNature Communications2041-17232023-10-0114111010.1038/s41467-023-42006-xSpectroscape enables real-time query and visualization of a spectral archive in proteomicsLong Wu0Ayman Hoque1Henry Lam2Department of Chemical and Biological Engineering, The Hong Kong University of Science and TechnologyDepartment of Chemical and Biological Engineering, The Hong Kong University of Science and TechnologyDepartment of Chemical and Biological Engineering, The Hong Kong University of Science and TechnologyAbstract 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.https://doi.org/10.1038/s41467-023-42006-x |
| spellingShingle | Long Wu Ayman Hoque Henry Lam Spectroscape enables real-time query and visualization of a spectral archive in proteomics Nature Communications |
| title | Spectroscape enables real-time query and visualization of a spectral archive in proteomics |
| title_full | Spectroscape enables real-time query and visualization of a spectral archive in proteomics |
| title_fullStr | Spectroscape enables real-time query and visualization of a spectral archive in proteomics |
| title_full_unstemmed | Spectroscape enables real-time query and visualization of a spectral archive in proteomics |
| title_short | Spectroscape enables real-time query and visualization of a spectral archive in proteomics |
| title_sort | spectroscape enables real time query and visualization of a spectral archive in proteomics |
| url | https://doi.org/10.1038/s41467-023-42006-x |
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