PXD006814

PXD006814 is an original dataset announced via ProteomeXchange.

Title	Optimization of quantitative proteomic analysis of clots
Description	The aim of our study was to optimize quantitative proteomic analysis of fibrin clots prepared ex vivo from citrated plasma of the peripheral blood drawn from patients with prior venous thromboembolism. We used a multiple enzyme digestion filter aided sample preparation (MED FASP) method combined with LC-MS/MS analysis performed on a Proxeon Easy-nLC System coupled to Q Exactive HF mass spectrometer. We also evaluated the impact of peptide fractionation with pipet-tip strong anion exchange (SAX) method on the obtained results. Our proteomic approach revealed >500 proteins repeatedly identified in the plasma fibrin clots from patients with venous thromboembolism. The multienzyme digestion (MED) FASP method using three different enzymes: LysC, trypsin and chymotrypsin increased the number of identified peptides and proteins and their sequence coverage as compared to a single and double step digestion. Peptide fractionation with SAX protocol slightly increased the depth of proteomic analyses, but also extended the time needed for sample analysis with LC-MS/MS.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:38:29.133.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jacek Wisniewski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-27 07:12:45	ID requested
1	2017-12-08 00:43:59	announced
⏵ 2	2024-10-22 04:38:33	announced	2024-10-22: Updated project metadata.

10.1186/s12014-017-9173-x;

Stachowicz A, Siudut J, Suski M, Olszanecki R, Korbut R, Undas A, Wi, ś, niewski JR, Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism. Clin Proteomics, 14():38(2017) [pubmed]

curator keyword: Biological

submitter keyword: proteomics, venous thromboembolism, clot, MED FASP

Jacek R Wisniewski
contact affiliation	Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
contact email	jwisniew@biochem.mpg.de
lab head
Jacek Wisniewski
contact affiliation	Proteomics
contact email	jwisniew@biochem.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2017/12/PXD006814

PRIDE project URI

• PRIDE
  1. PXD006814
     1. Label: PRIDE project
     2. Name: Optimization of quantitative proteomic analysis of clots