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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.
\n\nThis 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.
", "publication_date": "2018-09-05", "publisher": "Zenodo", "resource_type": { "id": "publication-article", "title": { "de": "Zeitschriftenartikel", "en": "Journal article" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "title": "Fast open modification spectral library searching through approximate nearest neighbor indexing" }, "parent": { "access": { "owned_by": { "user": 22786 } }, "communities": {}, "id": "3551508", "pids": {} }, "pids": { "doi": { "identifier": "10.1021/acs.jproteome.8b00359", "provider": "external" }, "oai": { "identifier": "oai:zenodo.org:3551509", "provider": "oai" } }, "revision_id": 2, "stats": { "all_versions": { "data_volume": 36295480.0, "downloads": 104, "unique_downloads": 102, "unique_views": 120, "views": 124 }, "this_version": { "data_volume": 35597490.0, "downloads": 102, "unique_downloads": 100, "unique_views": 117, "views": 121 } }, "status": "published", "updated": "2020-01-20T16:50:37.373588+00:00", "versions": { "index": 1, "is_latest": true } }