September 5, 2018 Journal article Open Access

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

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{
  "description": "<p>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. 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. 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 with SpectraST. 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>\n\n<p>This document is the unedited Author&#39;s version of a Submitted Work that was subsequently accepted for publication in the Journal of Proteome Research, copyright &copy; American Chemical Society after peer review. To access the final edited and published work see https://pubs.acs.org/articlesonrequest/AOR-Y7WnRgcWqx8vq5BR8gUu.</p>", 
  "license": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Department  of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium", 
      "@id": "https://orcid.org/0000-0002-3105-1359", 
      "@type": "Person", 
      "name": "Bittremieux, Wout"
    }, 
    {
      "affiliation": "Department  of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium", 
      "@id": "https://orcid.org/0000-0001-5903-633X", 
      "@type": "Person", 
      "name": "Meysman, Pieter"
    }, 
    {
      "affiliation": "Department of Genome Sciences, University of Washington, Seattle WA 98195, USA", 
      "@id": "https://orcid.org/0000-0001-7283-4715", 
      "@type": "Person", 
      "name": "Noble, William Stafford"
    }, 
    {
      "affiliation": "Department  of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium", 
      "@id": "https://orcid.org/0000-0002-8217-2564", 
      "@type": "Person", 
      "name": "Laukens, Kris"
    }
  ], 
  "headline": "Fast open modification spectral library searching through approximate nearest neighbor indexing", 
  "image": "https://zenodo.org/static/img/logos/zenodo-gradient-round.svg", 
  "datePublished": "2018-09-05", 
  "url": "https://zenodo.org/record/3551509", 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.1021/acs.jproteome.8b00359", 
  "@id": "https://doi.org/10.1021/acs.jproteome.8b00359", 
  "@type": "ScholarlyArticle", 
  "name": "Fast open modification spectral library searching through approximate nearest neighbor indexing"
}