**Abstract**

Stem cells represent a unique cell type that is capable of self-renewal and differentiation into somatic cell types. Since the derivation of human embryonic stem cells and induced pluripotent stem cells, enormous potential has been recognized for disease modeling, drug development and regenerative medicine. Both embryonic stem cells and induced pluripotent stem cells possess the ability to differentiate into all three germ layers, hence they are naturally prone to respond to various differentiation stimuli. These inherent cellular fluctuations, which can result in risky phenotypic instability, must be addressed prior to introduction of these cells to human medicine, since they represent one of the major biosafety obstacles in the development of bio-industrial or clinical-grade stem cell cultures. Therefore, there is an ongoing need for novel robust, feasible and sensitive methods for determination and confirmation of the otherwise identical cells status, as well as for the detection of hidden divergences from their optimal state. A method of choice can be the intact cell mass spectrometry. Here we show how it can be applied in routine quality control of embryonic stem cell cultures.

**Keywords:** intact cell mass spectrometry, whole cell mass spectrometry, embryonic stem cells, cell culture, culture adaptation, differentiation, quality control
