The cell envelope plays key roles in numerous processes such as maintaining cellular integrity, communication with other cells, signal transduction, maintenance of cellular homeostasis, and regulation of the traffic of molecules between the cell and the extracellular milieu. Essential membrane components in many of these processes are proteins. It is estimated that ~20-30% of the predicted open reading frames (ORFs) of all organisms encode membrane proteins. Furthermore, two thirds of drug targets are membrane proteins. However, despite their importance, membrane proteins have so far been mostly neglected in most proteomic studies, due to the inherent challenges in analyzing them.

The focus of this thesis is to devise strategies that allow investigation of membrane proteins and their associated complexes. Optimization of sample preparation in the underlying studies has allowed important goals to be reached in membrane protein analyses at various levels such as elucidation of their primary structure by collision-induced dissociation (CID) and electron-capture dissociation (ECD) mass spectrometry (MS), profiling membrane proteins and their complexes, the discovery of novel protein complexes, definition of their topology, and unambiguous identification of protein-bound ligand(s). This thesis paves the way for better characterization of membrane proteins and their assemblies hinting towards the crucial role(s) they play in maintaining normal cell physiology.