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DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2019-06-11
  • AnnouncementXML: Submission_2019-06-11_00:09:52.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Wout Bittremieux
  • Title: YPIC challenge 2018: A case study in characterizing an unknown protein sample
  • Description: For the YPIC challenge 2018 contestants were invited to try to decipher two unknown English questions encoded by a synthetic protein expressed in E. coli. We present how we analyzed this unknown sample using a tryptic digest with dynamic exclusion disabled to increase the signal-to-noise ratio of the measured molecules. Subsequently, spectral clustering was used to generate high-quality consensus spectra and condense the acquired MS/MS spectral data. De novo spectrum identification was used to determine the English questions encoded by the synthetic protein, and any post-translational modifications introduced by E. coli on the synthetic protein were detected using spectral networking. Although the synthetic protein sample for the YPIC challenge 2018 is not of biological interest, the experimental and computational strategy presented here can be directly used to analyze samples for which no protein sequence information is available. All software and code to perform the bioinformatics analysis is available as open source, and a self-contained Jupyter notebook is provided to fully recreate the analysis.
  • SpeciesList: scientific name: Escherichia coli; NCBI TaxID: 562;
  • ModificationList: acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
  • Instrument: Q Exactive

Dataset History

VersionDatetimeStatusChangeLog Entry
02019-05-24 03:18:33ID requested
12019-06-11 00:09:53announced

Publication List

  1. Dataset with its publication pending

Keyword List

  1. submitter keyword: YPIC, synthetic protein, de novo, spectral clustering, spectral networking

Contact List

    William Stafford Noble
    • contact affiliation: Department of Genome Sciences, University of Washington, Seattle, WA, USA
    • contact email: wnoble@uw.edu
    • lab head:
    Wout Bittremieux
    • contact affiliation: University of Antwerp
    • contact email: wout.bittremieux@uantwerpen.be
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
Repository Record List

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