Bittremieux, Wout
Meysman, Pieter
Noble, William Stafford
Laukens, Kris
2018-09-05
<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>
<p>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.</p>
https://doi.org/10.1021/acs.jproteome.8b00359
oai:zenodo.org:3551509
Zenodo
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Journal of Proteome Research, 17(10), 3463-3474, (2018-09-05)
Fast open modification spectral library searching through approximate nearest neighbor indexing
info:eu-repo/semantics/article