**1. Introduction**

Embryonic stem cells (ESCs) emerged as an amazing cell biology phenomenon several decades ago. Their derivation represents a milestone in understanding of fundamental molecular and cellular processes during early embryonic development, as well as differentiation mechanisms in somatic cells. Capacity of self-renewal and unlimited differentiation make the human ESCs (hESCs) a promising tool for regenerative medicine, tissue engineering, bio-industry, pharmacological modeling and pollutant testing. However, *in vitro* cultured ESCs suffer from inherent instability, and may develop unwanted properties over time, such as propensity to cancer development or failure of the functional phenotype. Accordingly, the stability of hESCs in long term cultures represents an essential prerequisite for a safe use in medical or industrial fields. Robust, sensitive and feasible tools are therefore required for efficient quality control of ESCs culture.

The beginnings in Mass Spectrometry (MS) development in biology correspond with the discovery of soft ionization techniques, such as Electrospray Ionization (ESI) and Matrix-Assisted Laser Desorption-Ionization (MALDI) by John Fenn (1988) and Koichi Tanaka (1988), respectively, who have been awarded with the Nobel Prize in chemistry in 2002 for these findings. MALDI MS coupled with Time-Of-Flight (TOF) analysis has been then successfully introduced to many fields beyond analytical chemistry, including proteomics, metabolomics, clinical microbiology and structural biology. MALDI TOF MS allows precise identification, structural analysis and quantification of various, predominantly soluble, analytes. MALDI TOF MS can generate molecular or spectral patterns that can be assigned to specific cell types or states, when intact cells are used as the analyte. Moreover it provides sufficient discrimination capacity due to a high variability in molecular species, constituting the whole spectrum a biomarker even without preceding peak identification.
