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We read the recent article “Proteinformatics: The New Trend in Tools” (August 2001) with interest. It provides a very helpful commentary on the various issues surrounding the informatics of mass spec data — but there’s plenty more meat on the bone of protein informatics. Below is a very brief summary of some our thoughts.

The rapidly evolving field of proteomics and associated informatics really needs much more sophisticated database searches to support protein characterization, for example, using annotations in sequence databases to refine computed masses of peptides; software that can interact with mass spec hardware to maximize productivity and minimize the amount of (redundant) data collected for routine identifications while supporting detailed data collection when required; seamless integration of mass spec data with other data including 2-DE gel databases; software to support functional validation of observed mRNA and/or protein expression changes; intelligent lab information management systems; integration of other data (including DNA array data, information from two hybrid screens, and structural databases) to supplement expression proteomics data.

One thing we discuss in a recent paper (Jenkins et al. Proteomics, in press) is the observation that DNA array data can be used to define the type of proteomics experiments that might be undertaken. For example, if DNA array experiments with model cell culture systems reveal changes in secreted proteins, then this component of the experimental system clearly needs to be included in any complementary proteomics experiments.

Finally, for those using 2-DE based expression proteomics the recent release of automated software for gel image analysis is being greeted with significant enthusiasm and relief — but only time will tell if it works effectively to reduce this significant informatics bottleneck.

These and other issues will give all those in protein informatics something to chew on for some time to come.

Stephen R. Pennington & Rosalind Jenkins, Department of Human Anatomy & Cell Biology, New Medical School, University of Liverpool

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