September 5, 2018 Journal article Open Access

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

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  <identifier identifierType="URL">https://zenodo.org/record/3551509</identifier>
  <creators>
    <creator>
      <creatorName>Bittremieux, Wout</creatorName>
      <givenName>Wout</givenName>
      <familyName>Bittremieux</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-3105-1359</nameIdentifier>
      <affiliation>Department  of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium</affiliation>
    </creator>
    <creator>
      <creatorName>Meysman, Pieter</creatorName>
      <givenName>Pieter</givenName>
      <familyName>Meysman</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5903-633X</nameIdentifier>
      <affiliation>Department  of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium</affiliation>
    </creator>
    <creator>
      <creatorName>Noble, William Stafford</creatorName>
      <givenName>William Stafford</givenName>
      <familyName>Noble</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7283-4715</nameIdentifier>
      <affiliation>Department of Genome Sciences, University of Washington, Seattle WA 98195, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Laukens, Kris</creatorName>
      <givenName>Kris</givenName>
      <familyName>Laukens</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8217-2564</nameIdentifier>
      <affiliation>Department  of Mathematics and Computer Science, University of Antwerp, 2020 Antwerp, Belgium</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Fast open modification spectral library searching through approximate nearest neighbor indexing</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <dates>
    <date dateType="Issued">2018-09-05</date>
  </dates>
  <resourceType resourceTypeGeneral="JournalArticle"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3551509</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1021/acs.jproteome.8b00359</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;This document is the unedited Author&amp;#39;s version of a Submitted Work that was subsequently accepted for publication in the Journal of Proteome Research, copyright &amp;copy; American Chemical Society after peer review. To access the final edited and published work see https://pubs.acs.org/articlesonrequest/AOR-Y7WnRgcWqx8vq5BR8gUu.&lt;/p&gt;</description>
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