Open AccessQuantitative proteomic analysis of trypsin‐treated extracellular vesicles to identify the real‐vesicular proteins
Author(s) -
Choi Dongsic,
Go Gyeongyun,
Kim DaeKyum,
Lee Jaewook,
Park SeonMin,
Di Vizio Dolores,
Gho Yong Song
Publication year - 2020
Publication title -
journal of extracellular vesicles
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.94
H-Index - 68
ISSN - 2001-3078
DOI - 10.1080/20013078.2020.1757209
Subject(s) - vesicular transport protein , microbiology and biotechnology , biology , golgi apparatus , endoplasmic reticulum , proteomics , trypsin , vesicle , membrane protein , protein targeting , quantitative proteomics , biochemistry , enzyme , membrane , gene
Extracellular vesicles (EVs) are nano‐sized vesicles surrounded by a lipid bilayer and released into the extracellular milieu by most of cells. Although various EV isolation methods have been established, most of the current methods isolate EVs with contaminated non‐vesicular proteins. By applying the label‐free quantitative proteomic analyses of human colon cancer cell SW480‐derived EVs, we identified trypsin‐sensitive and trypsin‐resistant vesicular proteins. Further systems biology and protein–protein interaction network analyses based on their cellular localization, we classified the trypsin‐sensitive and trypsin‐resistant vesicular proteins into two subgroups: 363 candidate real‐vesicular proteins and 151 contaminated non‐vesicular proteins. Moreover, the protein interaction network analyses showed that candidate real‐vesicular proteins are mainly derived from plasma membrane (46.8%), cytosol (36.6%), cytoskeleton (8.0%) and extracellular region (2.5%). On the other hand, most of the contaminated non‐vesicular proteins derived from nucleus, Golgi apparatus, endoplasmic reticulum and mitochondria. In addition, ribosomal protein complexes and T‐complex proteins were classified as the contaminated non‐vesicular proteins. Taken together, our trypsin‐digested proteomic approach on EVs is an important advance to identify the real‐vesicular proteins that could help to understand EV biogenesis and protein cargo‐sorting mechanism during EV release, to identify more reliable EV diagnostic marker proteins, and to decode pathophysiological roles of EVs.