Updated project metadata. The project aimed to determine proteomics changes in Bladder cancer (BCa) tissue from early to more advanced stages of the disease and identify the proteins associated with the progression. The samples used in this study were fresh frozen BCa tissues from patients collected immediately after surgery, with histopathologicaly confirmed disease. Samples were grouped according to the histopathological report in 3 groups: 1) Group 1 (pTa, G1), 2) Group 2 (T1, G2-G3) and 3) Group 3 (pT2-T3, G3). Patients were aged 28–82 years with no significant differences among groups regarding age: Median age (Group 1 (pTa, G1)) =62; Median age (Group 2 (T1, G2-G3)) =58 and Median age (Group 3 (pT2-T3, G3)) =73.5. Each group had 6 samples or 18 samples in total were used for the comparative proteomics analysis by label-free data-independent LC-MS/MS.