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PXD033117

PXD033117 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleEffect of Sample Transportation on the Proteome of Human Circulating Blood Extracellular Vesicles
DescriptionCirculating extracellular vesicles (cEV) are released by many kinds of cells and play an important role in cellular communication, signaling, inflammation modulation, coagulation and tumor growth. cEV are of growing interest, not only as biomarkers, but also as potential treatment targets. However, very little is known about the effect of transporting biological samples from the clinical ward to the diagnostic laboratory, notably on the protein composition. Pneumatic tube systems (PTS) and human carriers (C) are both routinely used for transport, subjecting the samples to different ranges of mechanical forces. We therefore investigated qualitatively and quantitatively the effect of transport by C and PTS on the human cEV proteome and particle size distribution. We found that samples transported by PTS were subjected to intense, irregular and multidirectional shocks, while those transported by C mostly underwent oscillations at a ground frequency of approximately 4 Hz. PTS resulted in the broadening of nanoparticle size distribution in platelet-free (PFP) but not in platelet-poor plasma (PPP). Cell-type specific cEV-associated protein abundances remained largely unaffected by the transport type. Since residual material of lymphocytes, monocytes, and platelets seemed to dominate cEV proteomes in PPP, it was concluded that PFP should be preferred for any further analyses. Differential expression showed that the impact of the transport method on cEV-associated protein composition was heterogeneous and likely donor-specific. Correlation analysis was nonetheless able to detect that vibration dose, shocks and imparted energy were associated with different terms depending on the transport, namely in C with cytoskeleton regulated cell organization activity, and in PTS with a release of extracellular vesicles, mainly from organelle origin, and specifically from mitochondrial structures. Feature selection algorithm identified proteins which, when considered together with the correlated protein-protein interaction network, could be viewed as surrogates of network clusters.
HostingRepositoryPRIDE
AnnounceDate2022-05-06
AnnouncementXMLSubmission_2022-05-06_05:40:36.054.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterManfred Heller
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListacetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-04-08 10:33:06ID requested
12022-05-06 05:40:36announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: circulating extracellular vesicles
pneumatical tube system transport
acceleration forces
vibration
label-free proteomics
clinical blood samples
Contact List
Manfred Heller
contact affiliationDepartment for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
contact emailmanfred.heller@dbmr.unibe.ch
lab head
Manfred Heller
contact affiliationProteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
contact emailpmscf@dbmr.unibe.ch
dataset submitter
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