Recently I posted a blog on using miRNA profiling as biomarkers for cancer. Protein profiling is another potential tool for hunting biomarkers. Traditional microarray data are based on the assumption that each individual protein contributes independently to clinical outcomes. As the data are inconsistent across different data sets, we start to think that not all proteins should be weighted equally. The first step is to identify the significant protein sets or pathways involved in disease, that is, the so called protein biomarkers.