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PXD001240

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2017-04-11
  • AnnouncementXML: Submission_2017-04-11_00:28:13.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Stefan Tenzer
  • Title: Benchmarking label-free quantification based on data-independent acquisition (DIA) workflows
  • Description: Label-free quantification based on data-independent acquisition (DIA) workflows is increasingly popular. Several software tools have been recently published or are commercially available. The present study focuses on the critical evaluation of three different software packages (Progenesis, synapter and ISOQuant) supporting ion-mobility enhanced DIA data. In order to benchmark the label-free quantification performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, E.coli). This model data set simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and down-regulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on the variation of reported protein quantities between technical replicates.
  • SpeciesList: scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
  • ModificationList: monohydroxylated residue; deaminated residue; iodoacetamide derivatized residue
  • Instrument: Synapt MS

Dataset History

VersionDatetimeStatusChangeLog Entry
02014-08-15 01:51:28ID requested
12015-01-07 04:59:11announced
22017-04-11 00:28:14announcedUpdated project metadata.

Publication List

  1. Kuharev J, Navarro P, Distler U, Jahn O, Tenzer S, In-depth evaluation of software tools for data-independent acquisition based label-free quantification. Proteomics, 15(18):3140-51(2015) [pubmed]

Keyword List

  1. curator keyword: Technical
  2. submitter keyword: Human, Yeast, E.coli

Contact List

    Stefan Tenzer
    • contact affiliation: University Medical Center Mainz, Institute for Immunology
    • contact email: tenzer@uni-mainz.de
    • lab head:
    Stefan Tenzer
    • contact affiliation: Institute for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.
    • contact email: tenzer@uni-mainz.de
    • dataset submitter:

Full Dataset Link List

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