Molecular Biology Commons^™

The Importance Of Experimental Design In Proteomic Mass Spectrometry Experiments: Some Cautionary Tales, Jeffrey S. Morris, Jianhua Hu, Kevin R. Coombes, Keith A. Baggerly

Jeffrey S. Morris

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 …