Spectroscape: Real-time Query and Visualization of a Spectral Archive of Millions of Tandem Mass Spectra

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 adapted an indexing algorithm developed by Facebook for organizing online multimedia resources to tandem mass spectra, and achieved practically instantaneous retrieval and spectrum 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 facilitate contextual validation of peptide identifications and exploration of the dark proteome.