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PXD038800

PXD038800 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleSize-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum
DescriptionExtracellular 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.
HostingRepositoryMassIVE
AnnounceDate2024-02-27
AnnouncementXMLSubmission_2024-02-26_23:40:21.620.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLuca Raess
SpeciesList scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationListOxidation; Carbamidomethyl; Acetyl
InstrumentOrbitrap Exploris 480
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-12-13 09:43:13ID requested
12024-02-26 23:40:21announced
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 affiliationBiognosys AG
contact emaillukas.reiter@biognosys.com
lab head
Luca Raess
contact affiliationBiognosys AG
contact emailluca.raess@biognosys.com
dataset submitter
Full Dataset Link List
MassIVE dataset URI
Dataset FTP location
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