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PXD001038

PXD001038 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleDifferentially embedded glioblastoma tumor protein quantitation
DescriptionGlioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a more physiologically relevant view of oncogenic signaling networks. However, clinical samples are not widely available and may be embedded for histopathologic analysis. With the goal of accurately identifying activated signaling networks in GBM tumor samples, we investigated the impact of embedding in optimal cutting temperature (OCT) compound followed by flash freezing in LN2 vs. immediate flash freezing (iFF) in LN2 on protein expression and phosphorylationmediated signaling networks. Quantitative proteomic and phosphoproteomic analysis of 8 pairs of tumor specimens revealed minimal impact of the different sample processing strategies and highlighted the large inter-patient heterogeneity present in these tumors. Correlation analyses of the differentially processed tumor sections identified activated signaling networks present in selected tumors and revealed the differential expression of transcription, translation, and degradation associated proteins. This study demonstrates the capability of quantitative mass spectrometry for identification of in vivo oncogenic signaling networks from human tumor specimens that were either OCT-embedded or immediately flash-frozen.
HostingRepositoryPRIDE
AnnounceDate2017-02-06
AnnouncementXMLSubmission_2017-02-06_01:12:54.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterHannah Johnson
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02014-06-05 08:40:59ID requested
12014-07-09 07:13:06announced
22014-07-24 05:19:34announcedUpdated project metadata.
32017-02-06 01:12:55announcedUpdated publication reference for PubMed record(s): 24927040.
Publication List
Johnson H, White FM, Quantitative analysis of signaling networks across differentially embedded tumors highlights interpatient heterogeneity in human glioblastoma. J Proteome Res, 13(11):4581-93(2014) [pubmed]
Keyword List
curator keyword: Biomedical
submitter keyword: Glioblastoma, Tumor, Protein expression, Quantitation, iTRAQ
Contact List
Forest M White
contact affiliationMassachuetts Institute of Technology
contact emailFWhite@MIT.EDU
lab head
Hannah Johnson
contact affiliationBabraham Institute
contact emailHannah.Johnson@Babraham.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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