Project PXD003209

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Proteomics of Extracellular Vesicles Harvested with ExtraPEG


Polyethylene glycol (PEG) is commonly used to isolate virus particles from culture medium. This project adapted and optimized the virus procedure for harvesting extracellular vesicles (of similar biophysical properties to viruses) from media. An 8% PEG solution harvested the purest vesicles. Followed by a wash step (ultracentrifugation of concentrated vesicles in saline), this method produced preparations comparable or superior to commonly used methods in terms of purity, abundance, and cost. It is also highly adaptable, allowing the procedure to be used for enriching vesicles from a variety of biological fluids. As proof of principle, extracellular vesicle protein was successfully harvested from HeLa cell medium using the described PEG-based harvest method and analyzed by mass spectrophotometry.

Sample Processing Protocol

HeLa cell extracellular vesicle proteins were harvested using the ExtraPEG protocol (8% Polyethylene Glycol precipitation of vesicles, followed by an ultracentrifugation wash of the re-suspended precipitates in saline; described above). Vesicles were lysed and proteins were harvested, quantified, and gel-purified. The pure proteins were trypsin digested in the gel. Eluted peptides were lyophilized prior to mass spectrophotometry analysis. The biosample was run with three technical replicates.

Data Processing Protocol

All .raw files were uploaded into proteome discoverer (Thermo Scientific, version and searched with Mascot and Sequest HT (version 2.4.0). Trypsin was selected as the enzyme and a maximum of 2 miss cleavages were permitted. Dynamic modifications were carbamiodomethyl (C residues), Oxidation (M residues), and Phosphorylation (S, T, and Y residues). The resulting .msf files (technical replicate) were then uploaded into the Scaffold software (Proteome Software, version Technical replicates were uploaded as an individual biosample, and data were searched with X!Tandem. All database searches used the swisprot human database with appended reverse sequences for target-decoy filtering, as well as a list of common contaminants of proteomics experimts (Contaminant sequences in the common Repository of Adventitious Proteins [cRAP] were downloaded from the Global Proteome Machine website). In Scaffold, the protein FDR was set to 1.0%, the peptide FDR was set to 1.0%, and the minimum number of peptides was set to 2.


Mark Rider, Florida State University
David G. Meckes Jr., Department of Biomedical Sciences, Florida State University College of Medicine, USA ( lab head )

Submission Date


Publication Date



    Rider MA, Hurwitz SN, Meckes DG Jr. ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles. Sci Rep. 2016 Apr 12;6:23978 PubMed: 27068479


Showing 1 - 3 of 3 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 62178 no assay title provided (mzIdentML) 6520 13527 10146 11774 11773
2 62176 no assay title provided (mzIdentML) 6738 13758 10234 11877 11875
3 62177 no assay title provided (mzIdentML) 6956 13870 10257 11909 11906