**6. Conclusions**

Intact Cell MALDI TOF MS reliably discriminates functionally different, but otherwise identical types or subtypes of stem cells of common genetic origin. Moreover, it reveals aberrant or differentiating clones of clinically relevant stem cells or committed tissue progenitors. Coupling the outputs of Intact Cell MALDI TOF MS with sophisticated statistics, such as cluster analysis or machine learning, may provide a feasible and easy-to-use routine tool for quality control of pluripotent stem cells and progenitors long-term cultures.
