Analysis code and MALDI-MSI input data for: Mass spectrometry and machine learning for classification and molecular phenotyping of renal cell carcinoma and benign tumors

R code for the analyses in “Mass spectrometry and machine learning for classification and molecular phenotyping of renal cell carcinoma and benign tumors” (Molecular & Cellular Proteomics, MCPRO-D-26-00216R1). The archive contains scripts for (i) LC-MS/MS (diaPASEF, DIA-NN) data import, filtering, imputation, differential abundance, patient-grouped random forest classification, leave-one-patient-out cross-validation, enrichment and survival analysis; and (ii) MALDI-MSI analysis from the peak-picked intensity matrix (unsupervised analysis, batch-correction comparison, patient-grouped random forest classification, leave-one-patient-out cross-validation chRCC vs OC). The LC-MS/MS raw data and DIA-NN outputs are deposited in PRIDE (PXD075682). The peak-picked MALDI-MSI intensity matrix (618,703 pixels × 868 m/z features) and de-identified pixel metadata are included as input to the MSI scripts. See README.md for run order and requirements.