Mass Spectrometry as an Emerging Tool for Systems Biology

Completion of the human genome project has created a blueprint of the genes and proteins necessary to construct and maintain a complex organism. Understanding how the molecular entities of human cells and tissues function will require sophisticated experiments to decipher how these molecules interact as a system. Beyond genes and proteins, metabolites encompass another important level of the system. To understand cellular systems, high-throughput strategies to investigate the functions of proteins and metabolites within the context of the system are necessary. Thus, understanding gene function (and ultimately biological systems) will require methods to broadly and quickly determine how the amounts and forms of various molecules are changing (Figure 1). Three considerations are relevant: (i) broad and unbiased measurement tools; (ii) comprehensive separation techniques; and (iii) informatics to analyze the data. This article will discuss mass spectrometry for the measurement of proteins and metabolites.