To better understand the mechanisms of TiO₂ nanoparticle (NP) uptake and toxicity in aquatic organisms, we investigated the interaction of NPs with the proteins found in gill mucus from blue mussels. Mucus is secreted by many aquatic organisms and is often their first line of defense against pathogens, xenobiotics, and other sources of environmental stress. Here, five TiO₂ NPs and one SiO₂ NP were incubated with gill mucus and run out on a one-dimensional polyacrylamide gel for a comparative qualitative analysis of the free proteins in the mucosal solution and the proteins bound to NPs. We then used nanoscale liquid chromatography coupled with tandem mass spectrometry to identify proteins of interest. Our data demonstrated dissimilar protein profiles between the crude mucosal solution and proteins adsorbed on NPs. In particular, extrapallial protein (EP), one of the most abundant mucus proteins, was absent from the adsorbed proteins. After thermal denaturation experiments, this absence was attributed to the EP content in aromatic amino acids that prevents protein unfolding and thus adsorption on the NP. Moreover, although the majority of the protein corona was qualitatively similar across the NPs tested here (SiO₂ and TiO₂), a few proteins in the corona showed a specific recruitment pattern according to the NP oxide (TiO₂ vs SiO₂) or crystal structure (anatase TiO₂ vs rutile TiO₂). Therefore, protein adsorption may vary with the type of NP. Graphical abstract Proteins with adsorption selectivity as identified from isolated bands.