FFPE proteome analysis of non-cancer lesion of renal cell carcinoma

To extract the molecules that correlate with kidney function and fibrosis, we performed the proteome analysis of non-cancer lesion of renal cell carcinoma in 16 patients. Proteins were extracted from FFPE slice samples and digested using the SP3 method as previously described. The digested peptide samples were analyzed by DIA-MS on a 6600 TripleTOF interfaced to Eksigent NanoLC400 system. Protein identification and quantification were performed using the library-free search function DIA-NN 1.9.2, with the UniProt human reference proteome allowing one miscleavage. The intensities of the precursors were normalized using retention time-dependent cross-run normalization. Peptides and proteins were filtered at a false discovery rate of < 1% for identification and quantification.