Using Nautilus to Capture Metadata for Identification of Protein Interactions
Auberry DL, V Kery, BS Hooker, WR Cannon, and HS Wiley.
Presented by Deanna Auberry at Thermo Informatics World, Bonita Springs, FL on September 20, 2005. PNNL-SA-46394.
We are using Nautilus to track and share metadata for protein interaction networks. For the Genomes to Life project, Oak Ridge National Lab and Pacific Northwest National Lab are collaborating on a joint project to identify protein-protein interactions in the facultative anaerobic bacteria Shewanella oneidensis and Rhodopseudomonas palustris. One goal of the joint project is to use Nautilus as our information management system, and share interactor data. Endogenous pulldowns are done at ORNL and exogenous pulldowns are done at PNNL on the same bait proteins. Mass spectrometric analysis is performed at each facility respectively, and the resulting protein identifications are analyzed and interactors identified. Analysis of the interactors and further bioinformatic research is done by combining the identifications with the metadata captured in Nautilus. Different proteins are expressed depending upon the conditions under which a culture is grown. For example, S. oneidensis can grow in the presence or absence of oxygen and different proteins will be expressed which results in different pathways being followed for building block synthesis and metabolism. It is this difference in protein expression that is essential for understanding the mechanism by which these bacteria function. The combination of the culture condition information, for example, and the complement of interacting proteins identified under those conditions provides novel and useful data to add to our understanding of protein interaction pathways
