Renal cell carcinoma (RCC) is one of the top ten most common malignancies worldwide. The field of clinical proteomics has seen successes in recent years, and advancements in technology is making ever more possible the ability to answer clinical questions. This study used proteomics to investigate two key clinical questions in RCC biology. Firstly, two comparative studies were performed to investigate biomarkers that may predict response to sunitinib, the predominant drug used to treat metastatic RCC. Serum (12 patients) and FFPE tissue (16 patients) samples from sunitinib responding and non-responding patients were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), to discover novel markers of response. Two candidate biomarkers were initially validated using Western blot or immunohistochemistry. Two serum (IGFBP5, CDH1) and two FFPE tissue (CD70, hCAP18) proteins were identified as promising candidate biomarkers, initial validation of CD70 and hCAP18 was performed. Secondly, furthering the understanding of RCC biology may improve rational drug design and biomarker identification. Five cell lines carrying mutations of VHL, the predominant tumour suppressor gene in RCC, were compared to investigate the proteomic impact of VHL mutation. The scaffold protein IRS2 was identified as highly expressed in the absence of VHL, and this protein was initially validated by Western blot in in vitro cell lines. The techniques used in this study revealed logical biological alterations, of which three proteins were validated using an independent technique. Further validation of the identified proteins is on-going, with the hope that they may impact upon patient care. The advantages and disadvantages of the proteomic analysis of serum, FFPE tissue, and in vitro cell lines is discussed.