Journal article Open Access

Fast open modification spectral library searching through approximate nearest neighbor indexing

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

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  "DOI": "10.1021/acs.jproteome.8b00359", 
  "container_title": "Journal of Proteome Research", 
  "title": "Fast open modification spectral library searching through approximate nearest neighbor indexing", 
  "issued": {
    "date-parts": [
  "abstract": "<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</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</p>", 
  "author": [
      "family": "Bittremieux, Wout"
      "family": "Meysman, Pieter"
      "family": "Noble, William Stafford"
      "family": "Laukens, Kris"
  "page": "3463-3474", 
  "volume": "17", 
  "type": "article-journal", 
  "issue": "10", 
  "id": "3551509"
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