July 23, 2018 Presentation Open Access

Bittremieux, Wout; Meysman, Pieter; Noble, William Stafford; Laukens, Kris

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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.1319036", 
  "title": "Fast open modification spectral library searching through approximate nearest neighbor indexing", 
  "issued": {
    "date-parts": [
      [
        2018, 
        7, 
        23
      ]
    ]
  }, 
  "abstract": "<p>Open modification search (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>\n\n<p>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>\n\n<p>ANN-SoLo outperforms the state-of-the-art SpectraST spectral library search engine both in terms of speed and the number of identifications. On a previously published human cell line data set, ANN-SoLo confidently identifies 40% more spectra than SpectraST while achieving a speedup of an order of magnitude.</p>\n\n<p>ANN-SoLo is implemented in Python and C++. It is freely available under the Apache 2.0 license at https://github.com/bittremieux/ANN-SoLo.</p>", 
  "author": [
    {
      "family": "Bittremieux, Wout"
    }, 
    {
      "family": "Meysman, Pieter"
    }, 
    {
      "family": "Noble, William Stafford"
    }, 
    {
      "family": "Laukens, Kris"
    }
  ], 
  "id": "1319036", 
  "event-place": "Seattle, WA, USA", 
  "type": "speech", 
  "event": "Cascadia Proteomics Symposium"
}