Mass Informatics in Differential Proteomics

Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work in harmony. As a major component of systems biology, differential proteomics studies the differences between distinct but related proteomes such as normal versus diseased cells and diseased versus treated cells. High throughput mass spectrometry (MS) based analytical platforms are widely used in differential proteomics (Domon, 2006; Fenselau, 2007). As a common practice, the proteome is usually digested into peptides first. The peptide mixture is then separated using multidimensional liquid chromatography (MDLC) and is finally subjected to MS for further analysis. Thousands of mass spectra are generated in a single experiment. Discovering the significantly changed proteins from millions of peaks involves mass informatics. This paper introduces data mining steps used in mass informatics, and concludes with a descriptive examination of concepts, trends and challenges in this rapidly expanding field.