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ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart.

User's guide

• Installing ANN-SoLo
• Quickstart
• Running ANN-SoLo
• mzTab output
• Plotting SSMs
• ANN-SoLo parameters

References

• Wout Bittremieux, Pieter Meysman, William Stafford Noble, Kris Laukens. Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing. Journal of Proteome Research (2018). doi:10.1021/acs.jproteome.8b00359

• Wout Bittremieux, Kris Laukens, William Stafford Noble. Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units. Journal of Proteome Research (2019). doi:10.1021/acs.jproteome.9b00291

• Issar Arab, William E. Fondrie, Kris Laukens, and Wout Bittremieux. Semisupervised Machine Learning for Sensitive Open Modification Spectral Library Searching. Journal of Proteome Research (2023). doi:10.1021/acs.jproteome.2c00616