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Identifying Millions of Protein Modifications Using GPU-Powered Approximate Nearest Neighbor Searching

Wout Bittremieux, University of California San Diego

GTC 2020

Learn how scientists are using GPUs to investigate the protein modification landscape at an unprecedented scale and depth. Mass spectrometry is a high-throughput technique to measure proteins in complex biological samples. Unfortunately, a significant portion of the thousands of mass spectra that are generated during a proteomics experiment cannot be confidently identified. In many cases, unidentified spectra correspond to modified proteins, as only a limited number of modifications can be considered during spectrum identification to avoid a search-space explosion. We'll show how proteins carrying any type of modification can be identified efficiently using GPU-powered approximate nearest neighbor searching. The ANN-SoLo spectral library search engine makes it possible to identify millions of modified proteins, outperforming alternative search tools by several orders of magnitude.

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