Abstract Extracellular vesicles (EVs) in blood plasma are recognized as potential biomarkers for disease. Although blood plasma is easily obtainable, analysis of EVs at the single particle level is still challenging due to the biological complexity of this body fluid. Besides EVs, plasma contains different types of lipoproteins particles (LPPs), that outnumber EVs by orders of magnitude and which partially overlap in biophysical properties such as size, density and molecular makeup. Consequently, during EV isolation LPPs are often co‐isolated. Furthermore, physical EV‐LPP complexes have been observed in purified EV preparations. Since co‐isolation or association of LPPs can impact EV‐based analysis and biomarker profiling, we investigated the presence and formation of EV‐LPP complexes in biological samples by using label‐free atomic force microscopy, cryo‐electron tomography and synchronous Rayleigh and Raman scattering analysis of optically trapped particles and fluorescence‐based high sensitivity single particle flow cytometry. Furthermore, we evaluated the impact on flow cytometric analysis in the presence of LPPs using in vitro spike‐in experiments of purified tumour cell line‐derived EVs in different classes of purified human LPPs. Based on orthogonal single‐particle analysis techniques we demonstrate that EV‐LPP complexes can form under physiological conditions. Furthermore, we show that in fluorescence‐based flow cytometric EV analysis staining of LPPs, as well as EV‐LPP associations, can influence quantitative and qualitative EV analysis. Lastly, we demonstrate that the colloidal matrix of the biofluid in which EVs reside impacts their buoyant density, size and/or refractive index (RI), which may have consequences for down‐stream EV analysis and EV biomarker profiling.
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