The dynamics of the thiol-disulphide redox proteome is central to cell function and its regulation. Altered mobility of proteins in the oxidized and reduced state allows the MS-based identification of those thiol-disulphide proteins that undergo major conformational changes. A proteomic approach was taken with thylakoid-bound, luminal and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-less stromal subproteome fractions of the chloroplast from Arabidopsis thaliana. Among the 49 verified polypeptides were 22 novel redox proteins, previously not reported as being part of the redox proteome. Among the redox-affected proteins were PsbA (D1), PsaA1 and PsaF, chloroplast monodehydroascorbate reductase and also the Deg1 protease. Recombinant Deg1 and Deg2 revealed redox dependence of their proteolytic activity. The data provide new insights into the redox network of the chloroplast.