Database SWISS-2DPAGE

FIGURE 1.1 A 2D-gel electrophoresis map of colorectal epithelia cells proteins from the SWISS- 2DPage database (entry CATD HUMAN, primary access number P07339) accessible from http //www.expasy.org/swiss-2dpage. 

SWISS-2DPAGE Human 2D Gel Protein Database from University of Geneva (SWISS-2DPAGE)... 

D. Appel, D. F. Hochstrasser. Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases the example of Escherichia coli. Electrophoresis. 

The entries in a federated 2-DE database like SWISS-2DPAGE contain active hyperlinks to cross-referenced databases, like SWISS-PROT and GeneBank. 

Annotations may also be exported to external, non-proprietary databases. For example, one can export the accession numbers of all identified proteins and automatically upgrade the SWISS-2DPAGE database. 

The links provided by the SWISS-PROT entries to other proteomics databases like SWISS-2DPAGE, PROSITE/InterPro and about 30 other databases allow for rapid access to experimental proteomic data, like position and number of protein spots on a 2-D gel, other members of the same family, or the 3-D structure of the protein, etc. 

The major advantages of this robotised approach are the limitation of human interventions, thus an increase in reproducibility and a decrease of the number of potential human errors. In our laboratory, this procedure currently yields a throughput of 400 fully analyzed spots per person and per week. The bottleneck is the validation step, because each individual protein identification has to be validated manually before being introduced into the SWISS-2DPAGE database. 

Fig. 1. Gel-separated proteins in human kidney from the SWISS-2DPAGE database (http // www.expasy.org/swiss-2dpage/). In the early 1980s, detecting any species above 5000 Da (right to the dashed line) was an insurmountable challenge for mass spectrometry. Yet gel electrophoresis showed that a wealth of information was available on crucial biomedical species in this region. The lack of efficient ion sources for these molecules started a decade-long race to produce gas-phase ions from ever larger molecules.

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