PXD036748

PXD036748 is an original dataset announced via ProteomeXchange.

Title	Towards optimised extracellular vesicle proteomics from cerebrospinal fluid
Description	The proteomic profile of extracellular vesicles (EVs) from cerebrospinal fluid (CSF) can reveal novel biomarkers for diseases of the brain. Here, we validate an ultrafiltration combined with size-exclusion chromatography (UF-SEC) method for isolation of EVs from canine CSF and probed the effect of starting volume for the EV proteomics profile. Using proteomics, SEC fractions 3-5 were compared and enrichment of EV markers in fraction 3 was detected, whereas fractions 4-5 contained more apolipoproteins. Lastly, we compared starting volumes of pooled CSF (6ml, 3ml, 1ml, and 0.5ml) to evaluate the effect on the proteomic profile. A total of 180 proteins was shared regardless of the starting volume. With a 0.5ml starting volume, 743 ± 77 or 345 ± 88 proteins were identified depending on the MaxQuant settings (with and without ‘match between runs’ active). The results confirm that UF-SEC effectively isolates CSF EVs and that EV proteomic analysis can be performed from 0.5ml of canine CSF.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:56:24.458.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tuula Nyman
SpeciesList	scientific name: Canis familiaris (Dog) (Canis lupus familiaris); NCBI TaxID: 9615;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF fleX

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-14 14:27:51	ID requested
1	2023-07-20 11:34:54	announced
2	2023-11-14 09:03:25	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 05:56:27	announced	2024-10-22: Updated project metadata.

Kangas P, Nyman TA, Mets, ä, honkala L, Burns C, Tempest R, Williams T, Karttunen J, Jokinen TS, Towards optimised extracellular vesicle proteomics from cerebrospinal fluid. Sci Rep, 13(1):9564(2023) [pubmed]

10.1038/s41598-023-36706-z;

submitter keyword: proteomics, ultrafiltration combined with size-exclusion chromatography, extracellular vesicles,cerebrospinal fluid

Tuula Nyman
contact affiliation	Head of Proteomics
contact email	tuula.nyman@medisin.uio.no
lab head
Tuula Nyman
contact affiliation	University of Oslo
contact email	tuula.nyman@medisin.uio.no
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/2023/07/PXD036748

PRIDE project URI

• PRIDE
  1. PXD036748
     1. Label: PRIDE project
     2. Name: Towards optimised extracellular vesicle proteomics from cerebrospinal fluid