September 5, 2018 Journal article Open Access

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

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  <dc:creator>Bittremieux, Wout</dc:creator>
  <dc:creator>Meysman, Pieter</dc:creator>
  <dc:creator>Noble, William Stafford</dc:creator>
  <dc:creator>Laukens, Kris</dc:creator>
  <dc:date>2018-09-05</dc:date>
  <dc:description>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.

This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in the Journal of Proteome Research, copyright © American Chemical Society after peer review. To access the final edited and published work see https://pubs.acs.org/articlesonrequest/AOR-Y7WnRgcWqx8vq5BR8gUu.</dc:description>
  <dc:identifier>https://zenodo.org/record/3551509</dc:identifier>
  <dc:identifier>10.1021/acs.jproteome.8b00359</dc:identifier>
  <dc:identifier>oai:zenodo.org:3551509</dc:identifier>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>https://creativecommons.org/licenses/by/4.0/legalcode</dc:rights>
  <dc:source>Journal of Proteome Research 17(10) 3463-3474</dc:source>
  <dc:title>Fast open modification spectral library searching through approximate nearest neighbor indexing</dc:title>
  <dc:type>info:eu-repo/semantics/article</dc:type>
  <dc:type>publication-article</dc:type>
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