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      Fast Open Modification Spectral Library Searching through Approximate Nearest Neighbor Indexing

      1 , 2 , 3 , 1 , 2 , 3 , 4 , 1 , 2

      Journal of Proteome Research

      American Chemical Society (ACS)

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          Abstract

          <p class="first" id="P1">Open modification searching (OMS) is a powerful search strategy that identifies peptides carrying any type of modification by allowing a modified spectrum to match against its unmodified variant by using a very wide precursor mass window. A drawback of this strategy, however, is that it leads to a large increase in search time. Although performing an open search can be done using existing spectral library search engines by simply setting a wide precursor mass window, none of these tools have been optimized for OMS, leading to excessive runtimes and suboptimal identification results. </p><p id="P2">Here we present the ANN-SoLo tool for fast and accurate open spectral library searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up OMS by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This approach is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate, as well as a shifted dot product score to sensitively match modified spectra to their unmodified counterparts. </p><p id="P3">ANN-SoLo achieves state-of-the-art performance in terms of speed and the number of identifications. On a previously published human cell line data set, ANN-SoLo confidently identifies more spectra than SpectraST or MSFragger and achieves a speedup of an order of magnitude compared to SpectraST. </p><p id="P4">ANN-SoLo is implemented in Python and C++. It is freely available under the Apache 2.0 license at <a data-untrusted="" href="https://github.com/bittremieux/ANN-SoLo" id="d531044e165" target="xrefwindow">https://github.com/bittremieux/ANN-SoLo</a>. </p>

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          Author and article information

          Journal
          Journal of Proteome Research
          J. Proteome Res.
          American Chemical Society (ACS)
          1535-3893
          1535-3907
          October 05 2018
          October 05 2018
          September 05 2018
          October 05 2018
          : 17
          : 10
          : 3463-3474
          Affiliations
          [1 ]Department of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium
          [2 ]Biomedical Informatics Network Antwerpen (biomina), 2020 Antwerp, Belgium
          [3 ]Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
          [4 ]Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
          Article
          10.1021/acs.jproteome.8b00359
          6173621
          30184435
          © 2018

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