Protein Expression Mapping

Conclusions

Protein expression mapping using 2D gel electrophoresis and mass spectrometry is the experimental strategy most often associated with the term proteomics. This approach is becoming widely used because of the desire to examine protein levels directly and because the instrumentation necessary for these experiments is readily available. As discussed above, protein expression mapping is often performed in conjunction with RNA expression studies using microarray technology. However, several limitations currently impede the progress of protein expression mapping. For example, the sensitivity and reproducibility of 2D gel electrophoresis does not match that of microarray technology (Gmuender et al., 2001; Gygi et al., 2000). In addition, quantitative analysis is difficult because the same protein can be found in many different spots on a 2D gel and because mass spectrometry cannot be used for quantitation without a reference point provided by isotope labeling (Gauss et al., 1999; Gygi et al., 1999). However, recent advances such as the in vitro ICAT-labeling strategy may solve many of these problems. The ability to fractionate, identify and quantitate proteins from complex samples by coupling ICAT-labeling with mass spectrometry has the potential to improve both throughput and reproducibility because fewer manipulations are required. In addition, the ICAT method could lead to improved detection of proteins that are present in low amounts in samples because, in contrast to 2D gel electrophoresis, any amount of starting material can be used.