Fig. 1

Schematic overview of the experimental workflow for the mass spectrometry part of study I and II. In study I, the protein content of exosomes from healthy individuals was analysed. Protein extracted from the isolated exosomes was subjected to strong cation exchange chromatography fractionation before analysis with a nano LC–MS/MS instrument. After the first acquisition all identified peptides were used to construct an exclusion list that was applied during the second acquisition. This was repeated for the third acquisition. Study II aimed to explore quantitative differences in the protein content of exosomes from respiratory diseases. The digested peptides were labelled with TMT reagents and subjected to fractionation before being analysed by nano LC–MS/MS. The resulting spectra from both study I and study II were searched in a database for identities and the reporter ions from the TMT reagents were used to quantify proteins in study II. All datasets were analysed with Ingenuity Pathways Analysis and GO Term Finder to identify enriched and associated cellular components, biological functions and processes