Although the human genome has now been completely sequenced, we are still a long way from defining all of the functional genes, and from a full understanding of the functions of the proteins encoded by these genes and the complex biological systems in which they're involved. A fundamental concept called the "proteome" (PROTEin complement to a genOME) has emerged over the past few years, and proteomics is a new discipline which complements physical genomic research, by comparing the proteomes of various structures and systems under different conditions to further unravel biological processes.

The basic steps in the proteomic analyses carried out collaboratively by the Lamond and Mann laboratories include purification of a protein complex or subnuclear structure from cultured mammalian cells, separation of the proteins by 1- or 2-dimensional polyacrylamide gel electrophoresis and/or direct LC/MS separation, identification of the proteins by peptide mass fingerprinting and mass spectrometry and bioinformatic analyses (cross-reference of protein informatics with genomic databases). Identified proteins are then further characterized by expression in mammalian and bacterial cells, generation of antibodies, etc. For more information about nuclear substructure and purification of subnuclear bodies, visit the Lamond lab website. For more information about mass spectrometry, visit the Mann lab website and the Center for Experimental Bioinformatics.

Listed below are publications relating to the nucleolar proteomics collaboration and the SILAC method for quantitative mass spectrometry.

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Publications relating to the nucleolar proteome and functional genomics

from our groups...

"Nucleolar proteome dynamics"; Andersen, J.S., Lam, Y.W., Leung, A.K.L., Ong, S.E., Lyon, C.E., Lamond, A.I. and Mann, M. (2005) Nature. 433:77-83.

"The Dynamics of the Nucleolus"; Leung, A.K.L. and Lamond, A.I. (2003) Critical Reviews in Eukaryotic Gene Expression. 13:49-64.

"Bioinformatic analysis of the nucleolus"; Leung, A.K.L., Andersen, J.S., Mann, M. and Lamond, A.I. (2003) Biochem. J., 376:553-69.

"Proteomics of the nucleolus"; Lam, Y.W., Fox, A.H., Leung, A.K.L., Andersen, J., Mann, M. and Lamond, A.I. (2003) In The Nucleolus, M. Olson Editor, Landes Bioscience, In Press.

"Directed Proteomic Analysis of the Human Nucleolus"; Andersen, J.S., Lyon, C.E., Fox, A., Leung, A., Lam, Y.W., Steen, H., Mann, M. and Lamond, A.I. (2002) Current Biology, 12:1-11.

"Functional genomics by mass spectrometry"; Andersen JS, Mann M. (2000) FEBS Lett. 480(1):25-31.

from other groups...

"Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire."; Staub, E., Fiziev, P., Rosenthal, A. and Hinzmann, B. (2004) Bioessays 5:567-581.

"Functional proteomic analysis of human nucleolus."; Scherl A., Coute Y., Deon C., Calle A., Kindbeiter K., Sanchez J.C., Greco A., Hochstrasser D., Diaz J.J. (2002) Mol Biol Cell. 11:4100-4109.

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Publications relating to the SILAC method

"Properties of 13C-substituted arginine in stable isotope labeling by aminoacids in cell culture (SILAC)"; Ong SE, Kratchmarova I, Mann M. (2003) J Proteome Res 2:173-81.

"Mass spectrometric-based approaches in quantitative proteomics"; Ong SE, Foster LJ, Mann M.(2003) Methods 2:124-30.

"Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics"; Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M. (2002) Mol Cell Proteomics 5:376-86.