The Importance of Experimental Design in Proteomic Mass Spectrometry Experiments: Some Cautionary Tales

Jeffrey S. Morris, The University of Texas M.D. Anderson Cancer Center
Jianhua Hu, The University of Texas M.D. Anderson Cancer Center
Kevin R. Coombes, The University of Texas M.D. Anderson Cancer Center
Keith A. Baggerly, The University of Texas M.D. Anderson Cancer Center

Abstract

Proteomic expression patterns derived from mass spectrometry have been put forward as potential biomarkers for the early diagnosis of cancer and other diseases. This approach has generated much excitement and has led to a large number of new experiments and vast amounts of new data. The data, derived at great expense, can have very little value if careful attention is not paid to the experimental design and analysis. Using examples from surfaceenhanced laser desorption/ionisation time-of-flight (SELDI-TOF) and matrix-assisted laser desorption–ionisation/time-of-flight (MALDI-TOF) experiments, we describe several experimental design issues that can corrupt a dataset. Fortunately, the problems we identify can be avoided if attention is paid to potential sources of bias before the experiment is run. With an appropriate experimental design, proteomics technology can be a useful tool for discovering important information relating protein expression to disease.