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In the course of a full-scale proteomics experiment, the handling of the data as well as the retrieval of the relevant information from the results is a major challenge due to the massive amount of generated data (gel images, chromatograms, and spectra) as well as associated result information (sequences, literature, etc.). To obtain meaningful information from these data, one has to filter the results in an easy way. Possibilities to do so can be based on GO terms or structural features such as transmembrane domains, involvement in certain pathways, etc.
In this presentation we will show how a combination of a software package with a workflow-based result organization (Bruker ProteinScape) and a protein-centered data-mining software (Proxeon ProteinCenter) can assist in the comparison of the results from large projects, such as comparison of cross-platform results from 2D PAGE/MS with shotgun LC-ESI-MS/MS. We will present differences between different technologies and show how these differences can be easily identified and how they allow us to draw conclusions on the involved technologies.