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PXD008783

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2018-07-11
  • AnnouncementXML: Submission_2018-07-11_08:11:01.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Hao Chi
  • Title: Open-pFind enables precise, comprehensive and rapid peptide identification in shotgun proteomics, part 2
  • Description: Shotgun proteomics has grown rapidly in recent decades, but a large fraction of tandem mass spectrometry (MS/MS) data in shotgun proteomics are not successfully identified. We have developed a novel database search algorithm, Open-pFind, to efficiently identify peptides even in an ultra-large search space which takes into account unexpected modifications, amino acid mutations, semi- or non-specific digestion and co-eluting peptides. Tested on two metabolically labeled MS/MS datasets, Open-pFind reported 50.5‒117.0% more peptide-spectrum matches (PSMs) than the seven other advanced algorithms. More importantly, the Open-pFind results were more credible judged by the verification experiments using stable isotopic labeling. Tested on four additional large-scale datasets, 70‒85% of the spectra were confidently identified, and high-quality spectra were nearly completely interpreted by Open-pFind. Further, Open-pFind was over 40 times faster than the other three open search algorithms and 2‒3 times faster than three restricted search algorithms. Re-analysis of an entire human proteome dataset consisting of ~25 million spectra using Open-pFind identified a total of 14,064 proteins encoded by 12,723 genes by requiring at least two uniquely identified peptides. In this search results, Open-pFind also excelled in an independent test for false positives based on the presence or absence of olfactory receptors. Thus, a practical use of the open search strategy has been realized by Open-pFind for the truly global-scale proteomics experiments of today and in the future.
  • SpeciesList: scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
  • ModificationList: No PTMs are included in the dataset
  • Instrument: Q Exactive

Dataset History

VersionDatetimeStatusChangeLog Entry
02018-01-29 01:39:15ID requested
12018-07-11 08:11:01announced

Publication List

  1. Dataset with its publication pending

Keyword List

  1. curator keyword: Technical
  2. submitter keyword: Open-pFind, metabolically label, yeast, Q Exactive HF

Contact List

    Si-Min He
    • contact affiliation: Institute of Computing Technology, CAS
    • contact email: smhe@ict.ac.cn
    • lab head:
    Hao Chi
    • contact affiliation: Institute of Computing Technology, CAS
    • contact email: chihao@ict.ac.cn
    • dataset submitter:

Full Dataset Link List

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