Upon contact with biota, nanoparticles can bind to proteins, which coat the nanoparticles and form a nanoparticle-protein corona. Knowledge of corona proteins is therefore important for a mechanistic understanding of how nanoparticles interact with biomolecules in cells. Here we present the first study to reveal the identity of corona proteins from silver nanoparticle (AgNPs)-exposed living vertebrate cells. The cells are from a rainbow trout (Oncorhynchus mykiss) gill cell line, RTgill-W1, representing the interface between the aquatic environment and one of its model species. Subcellular fractionation allowed AgNP-protein corona complexes to be recovered from intact subcellular compartments and proteins lysed from the AgNPs to be detected by mass spectrometry. The identified proteins mark the trail of AgNPs processing in the cells like a forensic fingerprint: the cells take up the AgNPs via endocytic processes and store the particles in endosomal/lysosomal compartments. Moreover, stress response proteins were recovered in the AgNPs protein corona. In this way, we established a list of AgNPs susceptible proteins which can be investigated further in targeted nanoparticle–protein interaction. As a proof of principle, we demonstrate that Na⁺/K⁺-ATPase, identified from the corona and a known key protein in ion regulation in gill cells, is inhibited in its activity by AgNPs, confirming previously published in vivo experiments. The developed methodology is broadly applicable to other nanoparticles and cell types, representing a valuable tool for mechanistic nanoparticle–cell interaction studies, ranging from environmental and human risk assessment to biomedicine. In this way, our research also contributes to safer particle design.