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PXD006291 is an original dataset announced via ProteomeXchange.

Dataset Summary

  • Title: HiRIEFII proteomics and proteogenomics of A431 cells and five histologically normal tissues
  • Description: High Resolution Isoelectric Focusing (HiRIEF) LC-MS was used to analyze samples from the human A431 cell line and also samples of histologically normal tissues. The high analytical depth afforded by HiRIEF permitted proteogenomics on these two sample sets (A431 cells and normal tissues). The A431 data was obtained from a time course experiment upon Gefitinib treatment (EGFR inhibition) of A431 cells with harvests at 2h, 6h and 24h after treatment as well of untreated cells. Isobaric tag labelling of peptide samples with TMT10plex was used. Biological triplicate controls (TMT channels 126, 127N, 127C), duplicate 2h (128N, 128C), duplicate 6h (129N, 129C) and triplicate 24h (130N, 130C, 131) samples were employed. The normal tissues data was obtained from two separate TMT10plex sets. TMT set1 was composed of 9 samples, all from different individuals, including three placenta samples (126, 127N, 127C) two liver samples (128N, 128C), two kidney samples (129N, 129C), two tonsil samples (130N, 130C), plus an internal pooled standard (131). TMT set2 was composed of 8 samples, all from different individuals, including one tonsil sample (126), two liver samples (127C, 128N), two kidney samples (128C, 129N), three testis samples (129C, 130N, 130C), plus an internal pooled standard (131). The internal pooled standard was made by combining equal aliquots of the tryptic peptide mixtures from each of the 17 tissue samples.
  • HostingRepository: PRIDE
  • AnnounceDate: 2018-01-19
  • AnnouncementXML: Submission_2018-04-06_07:06:14.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original dataset
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Rui Branca
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
  • Instrument: Q Exactive

Dataset History

RevisionDatetimeStatusChangeLog Entry
02017-04-13 06:37:17ID requested
12018-01-19 05:02:37announced
22018-04-06 07:06:15announcedUpdated publication reference for PubMed record(s): 29500430.

Publication List

  1. Zhu Y, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtiö J, Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nat Commun, 9(1):903(2018) [pubmed]

Keyword List

  1. curator keyword: Biological
  2. submitter keyword: human, A431, kidney, placenta, testis, tonsil, liver

Contact List

    Janne Lehtiö
    • contact affiliation: Department of Oncology-Pathology, Karolinska Institutet, and Science For Life Laboratory, Stockholm, Sweden
    • contact email: janne.lehtio@ki.se
    • lab head:
    Rui Branca
    • contact affiliation: Clinical Proteomics Unit, Dep. of Oncology-Pathology
    • contact email: rui.mamede-branca@ki.se
    • dataset submitter:

Full Dataset Link List

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

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