GUN1 proteins controls protein homeostasis in chloroplast development in cotyledons of the model plant Arabidopsis thaliana, via coordination of nuclear encoded polymerase (NEP)-dependent chloroplast genes expression with plastid encoded polymerase (PEP)-dependent chloroplast genes expression. Lack of GUN1 leads to development of abnormal plastids and, consequently, accumulation of nuclear-encoded chloroplast-targeted (NECT) proteins which in many cases have been found still in their precursor form. Data dependent acquisition (DDA) mass spectrometry analysis of cotyledons soluble fractions, as well as targeted proteomics analysis of specific FtsH protease forms recognized by FtsH antibodies in western blotting, have been performed to identify peptides from the chloroplast transit peptide (cTP) of NECT in cotyledons extracts of wild type and GUN1 knocked-out mutant plants. The aim was to compare the number of cTPs found in 6 days after sowing (DAS) seedlings grown on plates with or without the inhibitor of plastid translation lincomycin.