PXD038800-1
PXD038800 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum |
| Description | Extracellular vesicles (EVs) are important players in melanoma progression, but their use as clinical biomarkers has been limited by the difficulty of profiling blood-derived EV proteins with high depth of coverage, the requirement for large input amounts, and complex protocols. Here, we provide a streamlined and reproducible experimental workflow to identify plasma- and serum- derived EV proteins of healthy donors and melanoma patients using minimal amounts of sample input. SEC-DIA-MS couples size-exclusion chromatography to EV concentration and deep-proteomic profiling using data-independent acquisition. From as little as 200 µl of plasma per patient in a cohort of three healthy donors and six melanoma patients, we identified and quantified 2’896 EV-associated proteins, achieving a 3.5-fold increase in depth compared to previously published melanoma studies. To compare the EV-proteome to unenriched blood, we employed an automated workflow to deplete the 14 most abundant proteins from plasma and serum and thereby approximately doubled protein group identifications versus native blood. The EV proteome diverged from corresponding unenriched plasma and serum, and unlike the latter, separated healthy donor and melanoma patient samples. Furthermore, known melanoma markers such as MCAM, TNC, and TGFBI were upregulated in melanoma EVs but not in depleted melanoma plasma, highlighting the specific information contained in EVs. Overall, EVs were significantly enriched in intact membrane proteins and proteins related to SNARE protein interactions and T cell biology. Taken together, we demonstrated the increased sensitivity of an EV-based proteomic workflow that can be easily applied to larger melanoma cohorts and other indications. |
| HostingRepository | MassIVE |
| AnnounceDate | 2024-02-27 |
| AnnouncementXML | Submission_2024-02-26_23:40:21.620.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Luca Raess |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Oxidation; Carbamidomethyl; Acetyl |
| Instrument | Orbitrap Exploris 480 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2022-12-13 09:43:13 | ID requested | |
| ⏵ 1 | 2024-02-26 23:40:21 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Extracellular vesicle, EV, exosome, melanoma, proteomics, mass spectrometry, liquid biopsies, plasma, serum, size-exclusion chromatography, SEC, biomarker |
Contact List
| Lukas Reiter | |
|---|---|
| contact affiliation | Biognosys AG |
| contact email | lukas.reiter@biognosys.com |
| lab head | |
| Luca Raess | |
| contact affiliation | Biognosys AG |
| contact email | luca.raess@biognosys.com |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive.ucsd.edu/v05/MSV000090893/ |
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