September 17, 2018 Poster Open Access

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

JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/255b056a-946c-4072-bb86-bdc9635639d1/Genome_Science_retreat_2018_Fast_open_modification_spectral_library_searching_through_approximate_nearest_neighbor_indexing.pdf"
      }, 
      "checksum": "md5:703694f8db388f4bda77b236453c1791", 
      "bucket": "255b056a-946c-4072-bb86-bdc9635639d1", 
      "key": "Genome_Science_retreat_2018_Fast_open_modification_spectral_library_searching_through_approximate_nearest_neighbor_indexing.pdf", 
      "type": "pdf", 
      "size": 1419753
    }
  ], 
  "owners": [
    22786
  ], 
  "doi": "10.5281/zenodo.1418398", 
  "stats": {
    "version_unique_downloads": 94.0, 
    "unique_views": 73.0, 
    "views": 76.0, 
    "version_views": 76.0, 
    "unique_downloads": 94.0, 
    "version_unique_views": 73.0, 
    "volume": 136296288.0, 
    "version_downloads": 96.0, 
    "downloads": 96.0, 
    "version_volume": 136296288.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.1418398", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.1418397", 
    "bucket": "https://zenodo.org/api/files/255b056a-946c-4072-bb86-bdc9635639d1", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.1418397.svg", 
    "html": "https://zenodo.org/record/1418398", 
    "latest_html": "https://zenodo.org/record/1418398", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.1418398.svg", 
    "latest": "https://zenodo.org/api/records/1418398"
  }, 
  "conceptdoi": "10.5281/zenodo.1418397", 
  "created": "2018-09-13T14:48:01.389439+00:00", 
  "updated": "2020-01-20T16:27:36.510906+00:00", 
  "conceptrecid": "1418397", 
  "revision": 5, 
  "id": 1418398, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.1418398", 
    "description": "<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.</p>\n\n<p>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.</p>\n\n<p>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 to SpectraST.</p>\n\n<p>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>", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "title": "Fast open modification spectral library searching through approximate nearest neighbor indexing", 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "1418397"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "1418398"
          }
        }
      ]
    }, 
    "publication_date": "2018-09-17", 
    "creators": [
      {
        "orcid": "0000-0002-3105-1359", 
        "affiliation": "University of Washington", 
        "name": "Bittremieux, Wout"
      }, 
      {
        "orcid": "0000-0001-5903-633X", 
        "affiliation": "University of Antwerp", 
        "name": "Meysman, Pieter"
      }, 
      {
        "orcid": "0000-0001-7283-4715", 
        "affiliation": "University of Washington", 
        "name": "Noble, William Stafford"
      }, 
      {
        "orcid": "0000-0002-8217-2564", 
        "affiliation": "University of Antwerp", 
        "name": "Laukens, Kris"
      }
    ], 
    "meeting": {
      "dates": "17-19 September 2018", 
      "place": "Leavenworth, WA, USA", 
      "title": "Department of Genome Sciences retreat"
    }, 
    "access_right": "open", 
    "resource_type": {
      "type": "poster", 
      "title": "Poster"
    }, 
    "related_identifiers": [
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.1418397", 
        "relation": "isVersionOf"
      }
    ]
  }
}