Advances in sequencing mass spectrometry technologies have revealed large genomic, transcriptomic and proteomic heterogeneity of tumors. However, it has often been difficult to pinpoint which of the changes are important drivers of tumor progression. At the same time there has been a shift towards digital pathology. Strategies will be discussed for integrating proteomics, transcriptomics, genomics and histopathology data to better understand tumor biology with the goal of developing diagnostics and treatments for cancer.