Profiling phosphoproteome landscape in circulating extracellular vesicles from microliters of biofluids through functionally tunable paramagnetic separation.

Many biological processes are regulated through dynamic protein phosphorylation. Monitoring disease-relevant phosphorylation events in circulating biofluids is highly appealing but also technically challenging. We introduce here a functionally tunable material and a strategy, extracellular vesicles to phosphoproteins (EVTOP), which achieves one-pot EV isolation, extraction and digestion of EV proteins, and enrichment of phosphopeptides, with only trace amount of starting biofluids. EVs are efficiently isolated by magnetic beads functionalized with Ti(IV) ions and a membrane-penetrating peptide, octa-arginine R8+, which also provide the hydrophilic surface to retain EV proteins during lysis. Subsequent on-bead digestion concurrently converts EVTOP to Ti(IV) ion-only surface for efficient enrichment of phosphopeptides for phosphoproteomic analyses. The streamlined, ultra-sensitive platform enabled us to quantify 500 unique EV phosphopeptides with only a few μL of plasma and over 1,200 phosphopeptides with 100 μL of cerebrospinal fluid (CSF). We explored its clinical application of monitoring the outcome of chemotherapy of primary central nervous system lymphoma (PCNSL) patients with small volume of CSF, presenting a powerful tool for broad clinical applications.