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Fast open modification spectral library searching through approximate nearest neighbor indexing

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

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  <identifier identifierType="DOI">10.5281/zenodo.1319036</identifier>
      <creatorName>Bittremieux, Wout</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-3105-1359</nameIdentifier>
      <affiliation>University of Washington</affiliation>
      <creatorName>Meysman, Pieter</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0001-5903-633X</nameIdentifier>
      <affiliation>University of Antwerp</affiliation>
      <creatorName>Noble, William Stafford</creatorName>
      <givenName>William Stafford</givenName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0001-7283-4715</nameIdentifier>
      <affiliation>University of Washington</affiliation>
      <creatorName>Laukens, Kris</creatorName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="">0000-0002-8217-2564</nameIdentifier>
      <affiliation>University of Antwerp</affiliation>
    <title>Fast open modification spectral library searching through approximate nearest neighbor indexing</title>
    <date dateType="Issued">2018-07-23</date>
  <resourceType resourceTypeGeneral="Text">Presentation</resourceType>
    <alternateIdentifier alternateIdentifierType="url"></alternateIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsDocumentedBy">10.1101/326173</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1319035</relatedIdentifier>
    <rights rightsURI="">Creative Commons Attribution Share Alike 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
    <description descriptionType="Abstract">&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;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.&lt;/p&gt;

&lt;p&gt;ANN-SoLo is implemented in Python and C++. It is freely available under the Apache 2.0 license at;/p&gt;</description>
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