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The proteome is the entire protein complement from the genome. The analysis of cell structure by this approach is aimed at identifying the molecular makeup of the organelles and molecular machinery of the eukaryotic cell. The proteome (complete protein, carbohydrate, and lipid make-up) of all organelles of the secretory and endocytic pathways as well as of mitochondria and peroxisomes of the eukaryotic cell is currently under analysis. A robotics based 2-D gel and mass spectrometric analysis of the protein constituents enables unambiguous identification of the proteins, lipids and their chemical modifications in embryonic and cellular developments in normal and disease states. Molecular characterization is by mass spectrometry (MALDI, triple quadrupole, QToF and Ion Trap) employing high sensitivity and highly selective resolving techniques (LC, CE, GC) coordinated with the development of differential labeling techniques.