Stem cells are of wide interest because of their unique biological properties, and their potential in a variety clinical application. To understand stem cell behaviour, including self renewal and differentiation under a range of experimental conditions, they should be studied using the widest possible range of molecular techniques. In this respect, proteomics takes a central position in characterizing proteins responsible for or associated with stem cell-specific function. In this presentation I will give an overview of proteomic techniques available for profiling of cells in general, and stem cells in particular. I will focus on approaches that are directed at uncovering classes of proteins that are potentially of most interest, plasma membrane proteins and phospho-proteins. I will present data showing what type of information can be obtained when dedicated sample preparation and mass spectrometric analyses are deployed.