In this study, we have profiled the protein content of intravascular thrombotic material from stroke patients in the acute stage by quantitative proteomics. To this end, thrombotic material obtained by intra-arterial thrombolysis from stoke patients with different etiologies by TOAST classification (atherotrombotic and cardioembolic) was processed and further underwent proteomics analysis. As a result, we report a number of novel protein biomarkers that may help in differentiating atherotrombotic from cardioembolic stroke