A review with 30 refs. Cellular engineering relies on the ability to decipher the genetic basis of various phenotypes. Emerging technologies for analyzing the biol. function of the information encoded in the genome of particular organisms and/or tissues focus on the monitoring of transcription (mRNA) and translation (protein) processes. Elementary theor. considerations presented in this article strongly suggest that a combination of mRNA and protein expression patterns should be simultaneously considered to fully develop a conceptual understanding of the functional architecture of genomes and gene networks. We propose a framework of exptl. and math. methods for acquiring and analyzing quant. proteomic information and discuss recent developments in proteome anal. technol. [on SciFinder (R)]