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DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2017-08-15
  • AnnouncementXML: Submission_2017-08-15_00:30:31.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Johannes Leufken
  • Title: pyQms - partial labeled proteome gold standard
  • Description: " The novel mass spectrometry quantitation tool pyQms can calculate isotope patterns for molecules that have any isotope enrichment or combinations of, e.g. 13C or 15N and allows partially labeled molecules to be quantified as well, as observed in pulse or pulse-chase experiments where enrichment levels change dynamically. In order to test how pyQms performs on such a task, we created a gold standard (GS) data set of partially labeled proteomes, which allows evaluation of algorithms detecting partial labeld isotopologues against the ground truth against 5 mixed samples. Cultures of Chlamydomonas reinhardtii were grown on medium containing 20, 40, 60, 80 and 100% 15N. Since partially labeled peptides will not produce interpretable fragmentation spectra, each of the partially labeled proteomes were mixed with an unlabeled (14N) or fully labeled (15N) proteome, yielding 5 mixed samples (0|100, 20|100, 40|100, 0|60 and 0|80). " (Modified from manuscript)
  • SpeciesList: scientific name: Chlamydomonas reinhardtii; NCBI TaxID: 3055;
  • ModificationList: monohydroxylated residue; acetylated residue
  • Instrument: Q Exactive

Dataset History

VersionDatetimeStatusChangeLog Entry
02015-11-25 04:49:32ID requested
12017-08-10 02:18:14announced
22017-08-15 00:30:32announcedUpdated project metadata.

Publication List

  1. Leufken J, Niehues A, Sarin LP, Wessel F, Hippler M, Leidel SA, Fufezan C, pyQms enables universal and accurate quantification of mass spectrometry data. Mol Cell Proteomics, 16(10):1736-1745(2017) [pubmed]

Keyword List

  1. curator keyword: Technical
  2. submitter keyword: LC-MS/MS, Gold standard dataset

Contact List

    Dr. Christian Fufezan
    • contact affiliation: Institute of Plant Biology and Biotechnology, University of Muenster, Germany
    • contact email: christian@fufezan.net
    • lab head:
    Johannes Leufken
    • contact affiliation: Max Planck Institute for Molecular Biomedicine RNA biology laboratory Von-Esmarch-Straße 54 48149 Münster Germany
    • contact email: johannes.leufken@uni-muenster.de
    • dataset submitter:

Full Dataset Link List

  1. Dataset FTP location
  2. PRIDE project URI
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