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Systems biology as the understanding and prediction of how intracellular machinery works, needs new technological support in order to observe cell metabolism at all its levels. From organism genome to its transcription to proteins and how these proteins regulate metabolite pools as a final response to determined stimuli, are needed to have a close look at specific metabolic states. Mass spectrometry is used to obtain intracellular information at a metabolomics, peptidomics and proteomics level for specific questions concerning bioprocesses optimization.