Quantitative mass spectrometry using iTRAQ was used to identify differentially expressed proteins from 16 colorectal cancer (CRC) tumours compared to patient-paired adjacent normal mucosa. Over 1400 proteins were identified and quantitated, with 118 determined as differentially expressed by >1.3-fold, with false discovery rate < 0.05. Gene Ontology analysis indicated that proteins with increased expression levels in CRC tumours include those associated with glycolysis, calcium binding, and protease inhibition. Proteins with reduced levels in CRC tumours were associated with loss of ATP production through: (i) reduced β-oxidation of fatty acids, (ii) reduced NADH production by the tricarboxylic acid cycle and (iii) decreased oxidative phosphorylation activity. Additionally, biosyntheses of glycosaminoglycans and proteoglycans were significantly reduced in tumour samples. Validation experiments using immunoblotting and immunohistochemistry (IHC) showed strong concordance with iTRAQ data suggesting that this workflow is suitable for identifying biomarker candidates. We discuss the uses and challenges of this approach to generate biomarker leads for patient prognostication.