PXD033117

PXD033117 is an original dataset announced via ProteomeXchange.

Title	Effect of Sample Transportation on the Proteome of Human Circulating Blood Extracellular Vesicles
Description	Circulating 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.
HostingRepository	PRIDE
AnnounceDate	2022-05-06
AnnouncementXML	Submission_2022-05-06_05:40:36.054.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manfred Heller
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-04-08 10:33:06	ID requested
⏵ 1	2022-05-06 05:40:36	announced

Dataset with its publication pending

submitter keyword: circulating extracellular vesicles

pneumatical tube system transport

acceleration forces

vibration

label-free proteomics

clinical blood samples

Manfred Heller
contact affiliation	Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
contact email	manfred.heller@dbmr.unibe.ch
lab head
Manfred Heller
contact affiliation	Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
contact email	pmscf@dbmr.unibe.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD033117
     1. Label: PRIDE project
     2. Name: Effect of Sample Transportation on the Proteome of Human Circulating Blood Extracellular Vesicles