One common approach to characterizing subcellular organelles uses high-throughput mass spectrometry to catalog each compartment's protein complement. The trouble is, the result is just a list, devoid of functional annotation, and possibly riddled with errors.
Søren Brunak of the Technical University of Denmark and colleagues have addressed this shortcoming, integrating existing proteomics and protein-protein interaction datasets with a novel "reverse proteomics" approach to produce a "first draft ... functional annotation of the human nucleolus," the authors write.
"Being able to combine the data from the proteomics with other more functional data, such as protein-protein interaction data, allows you to really put these protein complexes together and to identify pathways that are involved in a particular process," says Faculty of 1000 member Lucio Comai of the University of Southern California.
Though this study focused on ribosome biogenesis and the nucleolus, "I think the importance of this paper is that this type of analysis can be applied to a lot of other types of high-throughput mass spectrometry data" - that is, to other processes and organelles, Comai says. "It's becoming more and more evident that many nuclear processes appear to be localized to discrete subnuclear domains," he says; such domains could be ripe for this type of integrated analysis.1. A.M. Hinsby et al., "A wiring of the human nucleolus," Mol Cell, 22:285-95, April 21, 2006.