This project contains the proteomics dataset supporting the in vitro protein corona analysis of differently functionalized rare-earth-based nanoprobes. Raw LC-MS/MS files are provided for group B (COO-free NPs) and group C (NE-mimetic NPs), including biological replicates B1, B2, B3, C1, C2, and C3. The submission also includes peptide and protein identification files, sample-group information, and the processed quantitative analysis used for the manuscript. The figures and statistical comparisons derived from this dataset are based on groups B and C only.