Recently, we released a new version of our web-based ProteinCenter software which includes more than 223 million protein-protein interactions in its database and direct support for the popular Cytoscape open source platform. (Cytoscape is used to visualize complex networks in proteomics data.)
For the benefit of our customers, I had a question and answer email exchange with Christian Ravsborg, the Product Manager for the ProteinCenter software among other products. Christian is based in Odense, Denmark, which has been associated with proteomics research for more than a decade.
Sonya Pelia (SP): What are the challenges faced by scientists in proteomics studies today?
Christian Ravsborg (CR): One of the main challenges for scientists today is data interpretation because as instrument technology improves, it provides increasingly large amounts of data for interpretation of biological hypothesis. We find that scientists are using increasing amounts of time just crunching data. Another challenge in proteomics research are the protein sequence databases, which are key for a successful experiment, but they are highly inconsistent.
SP: Why are the inconsistent protein sequence databases used for protein identification in proteomics a challenge?
CR: Currently, many different protein sequence databases are used and in these repositories sequences, accession keys and names are changed frequently. This makes it very time consuming for scientists to compare their results against each other and publish their results. This makes it very time consuming for scientists to compare their results against each other and publish their results.
SP: How does ProteinCenter enable scientists to analyze data sets identified with inconsistent protein sequence database?
CB: The ProteinCenter software is based on a consolidated protein sequence and annotation database drawing for all the major protein repositories. This database is constantly updated enabling scientists to map proteins against different databases and their history. What this means for scientists is that they are able to easily and confidently compare their results with collaborators and publish data from their research.
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SP: What enhancements does ProteinCenter v3.8 provide to the database?
CB: With the addition of more than 200 million protein-protein interactions to our ProteinCenter database, proteomics scientists can quickly determine important protein binding partners for their identified proteins independent of the search database.
SP: How will the CytoScape support help scientists?
CR: With our direct support, scientists using our software solution can easily transfer their data into CytoScape. As Cytoscape is an open source software platform for visualizing complex networks, it can integrate any type of attributable data. A lot of plugins are available for various kinds of problem domains, including proteomics and genomics. Using CytoScape and the ProteinCenter database, scientists can now gain new insights to their proteomics data quickly and thus keep their focus on research rather than data interpretation.
SP: What other resources can you offer a scientist who might be stuck in the data analysis stage?
CR: One of our specialists can provide a free online data analysis.
Christian has also offered to respond to any questions you might have about this latest version of the software so don’t forget to add your questions in the Comments box below!