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PXD011353

PXD011353 is an original dataset announced via ProteomeXchange.

Dataset Summary

  • Title: PROTEOFORMER 2.0: MS validation
  • Description: PROTEOFORMER is a pipeline for generating a search space of candidate translation products based on ribosome profiling data. The pipeline was published in 2014, but since then, several features have been added. For this project, the PROTEOFORMER pipeline 2.0 was tested on human HCT116 and Jurkat cell ribosome profiling data with all its new features and then compared to raw MS data of both cell lines, validating its use as a proteogenomic tool. In this study, results of 3 proteoform calling methods were combined (classical PROTEOFORMER proteoform calling, PRICE and SPECtre). Afterwards, results were eventually combined with the canonical or splicing-included version of human UniProt. The different described combinations were exported as a FASTA file and used as search space for searching matching MS data.
  • HostingRepository: PRIDE
  • AnnounceDate: 2019-05-03
  • AnnouncementXML: Submission_2019-05-03_13:37:55.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original dataset
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Steven Verbruggen
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: monohydroxylated residue; acetylated residue
  • Instrument: Q Exactive

Dataset History

RevisionDatetimeStatusChangeLog Entry
02018-10-15 02:01:55ID requested
12019-05-03 13:37:56announced

Publication List

  1. Verbruggen S, Ndah E, Van Criekinge W, Gessulat S, Kuster B, Wilhelm M, Van Damme P, Menschaert G, PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms. Mol Cell Proteomics, 18(8 suppl 1):S126-S140(2019) [pubmed]

Keyword List

  1. curator keyword: Technical
  2. submitter keyword: HCT116, Jurkat, MSMS, PROTEOFORMER

Contact List

    Gerben Menschaert
    • contact affiliation: BioBix, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, Belgium
    • contact email: Gerben.Menschaert@UGent.be
    • lab head:
    Steven Verbruggen
    • contact affiliation: BioBix
    • contact email: Steven.Verbruggen@UGent.be
    • dataset submitter:

Full Dataset Link List

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