Assessing variability in gel-based proteomic analysis of Nitrosomonas europaea

Proteomics offers a unique look at the way protein expression changes in response to stimuli, and "gel-based" methods that utilize two-dimensional gel electrophoresis (2-DE) are key technologies in such studies. However, the many steps involved can be technically complex, and the resulting data are subject to variability from both technical and biological sources. Designing 2-DE proteomic studies can be challenging, as a set of standard methods or experimental designs has not been established. This being the case, it is especially important to identify and control sources of variability. Statistically significant results can be obtained if the experimental design includes a sufficient number of replicate 2-DE gels, and if the replicate gels are similar enough to be analyzed in the same experiment. While three or four replicates are often sufficient for compensation of variability, the pilot study illustrated in this chapter showed that statistically significant expression differences could be detected for 90% of the spots matched if six replicate experiments were done.