PXD003935

PXD003935 is an original dataset announced via ProteomeXchange.

Title	Profiling of Human Circulating Plasma Microparticle Associated Proteins by DDA and DIA
Description	Cells of the vascular system release spherical vesicles, called microparticles (MP), in the size range of 0.1-1μm induced by a variety of stress factors resulting in variable MP concentrations between health and disease. Furthermore, MP have intercellular communication/signaling properties and interfere with inflammation and coagulation pathways. Today’s most used analytical technology for MP characterization, flow cytometry, is lacking sensitivity and specificity, which might have led to the publication of contradicting results in the past. We propose the use of nano-liquid chromatography coupled to two-stage mass spectrometry as a non-biased tool for quantitative MP proteome analysis. Using aliquots of 250 μL platelet-free plasma (PFP) from one individual donor, we achieved excellent inter-assay CV’s of 2.7 ± 1.7% (mean ± 1 S.D.) on individual peptide intensities across 27 data-dependent nanoLC-MS/MS runs performed over a period of 3.5 months. With quantitative proteomics, we show that MP composition between twelve volunteers were remarkably stable. MP protein composition is clearly distinguishable from whole cell lysates and we propose that this trait should be used as a quality criterion of MP purity. Furthermore, MP were damaged by freezing PFP. The damage was articulated by a loss of cytoplasm proteins, encompassing a specific set of proteins involved in regulating dynamic structures of the cytoskeleton, and thrombin activation leading to MP clotting. On the other hand, plasma membrane protein composition (cell markers) was not affected. Finally, we show that multiplexed data-independent acquisition can be used for relative quantification of target proteins using Skyline software.
HostingRepository	PRIDE
AnnounceDate	2016-10-18
AnnouncementXML	Submission_2016-10-18_04:50:37.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	carbamoylated residue; phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-10 23:47:53	ID requested
⏵ 1	2016-10-18 04:50:38	announced

Braga-Lagache S, Buchs N, Iacovache MI, Zuber B, Jackson CB, Heller M, Robust Label-free, Quantitative Profiling of Circulating Plasma Microparticle (MP) Associated Proteins. Mol Cell Proteomics, 15(12):3640-3652(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, Plasma, Microparticles, Relative Quantification

Manfred Heller
contact affiliation	University of Bern, Department of Clinical Research, Proteomics and Mass Spectrometry Core Facility, 3010 Bern, Switzerland
contact email	manfred.heller@dkf.unibe.ch
lab head
Manfred Heller
contact affiliation	University of Bern
contact email	manfred.heller@dkf.unibe.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003935
     1. Label: PRIDE project
     2. Name: Profiling of Human Circulating Plasma Microparticle Associated Proteins by DDA and DIA