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Spectral library searching using approximate nearest neighbor techniques.
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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.
The software is available as open-source under the Apache 2.0 license.
If you use ANN-SoLo in your work, please cite the following publications:
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
See the wiki for detailed instructions on how to install and run ANN-SoLo.
ANN-SoLo requires Python 3.6 or higher. The GPU-powered version of ANN-SoLo can be used on Linux systems with an NVIDIA CUDA-enabled GPU device, while the CPU-only version supports both the Linux and OSX platforms. Please refer to the Faiss installation instructions linked below for more information on OS and GPU support.
The recommended way to install ANN-SoLo is using pip:
For more information you can visit the official code website or send an email to wout.bittremieux@uantwerpen.be.
Spectral library searching using approximate nearest neighbor techniques.

pip install ann-solo Copy PIP instructions
Spectral library search engine optimized for fast open modification searching
View statistics for this project via Libraries.io, or by using our public dataset on Google BigQuery
License: Apache Software License (Apache 2.0)
Cockroach Labs is a contributing sponsor of the Python Software Foundation.
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.
The software is available as open-source under the Apache 2.0 license.
See the wiki for detailed instructions on how to install and run ANN-SoLo.
ANN-SoLo requires Python 3.6 or higher. The GPU-powered version of ANN-SoLo can be used on Linux systems with an NVIDIA CUDA-enabled GPU device, while the CPU-only version supports both the Linux and OSX platforms. Please refer to the Faiss installation instructions linked below for more information on OS and GPU support.
The recommended way to install ANN-SoLo is using pip:
Run ANN-SoLo to search your spectral data directly using on the command line using ann_solo or as a named Python module (if you do not have sufficient rights to install command-line scripts) using python -m ann_solo.ann_solo.
ANN-SoLo arguments can be specified as command-line arguments or in a configuration file. Argument preference is command-line args > configuration file > default settings.
For more information on which arguments are available and their default values run ann_solo -h.
Most options have sensible default values. Some positional arguments specifying which in- and output files to use are required. Additionally, the precursor and fragment mass tolerances do not have default values as these are data set dependent.
Please note that to run ANN-SoLo in cascade search mode two different precursor mass tolerances need to be specified for both levels of the cascade search (precursor_tolerance_(mass|mode) and precursor_tolerance_(mass|mode)_open).
Use the ANN-SoLo plotter to visualize spectrum–spectrum matches from your search results. The plotter can be run directly on the command line using ann_solo_plot or as a named Python module (if you do not have sufficient rights to install command-line scripts) using python -m ann_solo.plot_ssm.
The plotter requires as command-line arguments an mzTab identification file produced by ANN-SoLo and the identifier of the query to visualize. Please note that the spectral library used to perform the search needs to be present in the exact location as specified in the mzTab file.
The plotter will create a PNG file with a mirror plot to visualize the specified spectrum–spectrum match.
For more information you can visit the official code website or send an email to wout.bittremieux@uantwerpen.be.
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