The LTQ-Orbitrap mass spectrometer was employed to continue our research aimed to understand the regulation of photosynthesis in response to various stresses in the green alga Chlamydomonas reinhardtii. For this purpose we further improved comparative proteomics approaches talking advantage of metabolic labeling strategies. We previously used comparative proteomics to identify candidate proteins involved in the response to iron-deficiency. In this regard we characterized the function of LHCSR3 and demonstrated that this protein is essential for energydependent non-photochemical quenching. To this end we employed mass spectrometry to characterize the content of light-harvesting proteins in wild-type and LHCSR3-deficient mutants. Comparative proteome analyses using stable isotope labeling of amino acids revealed insights into the anaerobic response of the green alga. The focus of the work was put on the chloroplast and more than 400 chloroplast proteins could be quantitated. In addition this work defined a core chloroplast proteome of C. reinhardtii consisting of 996 proteins . These localization data will provide an important basis for further functional studies and modeling purposes. Candidate anaerobic response genes that were identified by the comparative proteomics approach were investigated by reverse genetics employing RNAi and amiRNA approaches. These studies identified TEF7 as a new player in the anaerobic response since mutant strains having lower levels of this protein cannot survive under anaerobic growth conditions. Using comparative and absolute mass spectrometric quantitation, the composition of photosystem I and its associated light-harvesting proteins from the green alga C. reinhardtii and from the unicellular red alga Cyanidioschyzon merolae was investigated. In the course of the proteomic experiments, a new mass spectrometric evaluation pipeline for peptide and protein identification and quantitation was established and the mass spectrometric data were additionally utilized for a proteogenomic approach serving for improved annotation of the C. reinhardtii gene models. In an additional research line we established phospho-proteomics to map in vivo and in vitro protein phosphorylation sites using SIMAC fractionation (sequential elution from IMAC) and identification of the peptides and proteins by mass spectrometry using the MultiStage activation modus. This approach was utilized to determine phosphoproteins in the process of flagellar disassembly during flagellar shortening in Chlamydomonas. Furthermore we are engaged in the analysis of calcium signaling via protein phosphorylation in plant model cell types during environmental stress adaptation.