On characterization of 2-D proteomics maps

Milan Randic, National Institute of Chemistry, Ljubljana, Slovenia

Proteome has been defined as the totality of all proteins in cells of particular organ or tissue of living systems and proteomics research is concerned with identification, characterization, quantification and the study of interaction and function of proteins in a cell. Formally proteome is defined as PROTEin complement expressed by genOME (or tissue). The challenge is due to complexity of cells that typically contains thousands and thousands of proteins. Proteomics map is obtain by separating proteins by charge (electrophoretically) and by mass (chromatographically) on a 2-D gell. Such 2-D maps have been, and continue to be, examined mostly visually. I will review recent development of quantitative (numerical) approach for comparison of different 2-D maps based on construction of sets of map invariant, which are themselves obtained by associating with a 2-D map matrices based on embedded curves and embedded graphs (based either on partial ordering of protein spots by charge and mass, or based on clustering of spots which are at small distances. Numerical characterization of proteomics maps is viewed by some as potentially a major
breakthrough in the proteomics research. Although a characterization of 2-D proteomics maps is considering just one of many aspects of the proteomics research it is likely to help in answering other complex problems, including the study of the function of interacting proteins within a single cell. The question "Where do we come
from and where are we going to?" relating to Life on a macroscale may well benefit from the question "Where do we come from and where are we going to?" relating to Cells on a microscale - which is the central question to the Proteome Research.