Using a Protein Engineering Analysis Tool to Capture, and Analyze Experimental Data

The scientists, from University College Dublin (UCD) Conway Institute (Dublin, Ireland), led by Conway fellow, Dr. Jens Erik Nielsen, described the application in an article published online August 19, 2010, in the journal Nucleic Acids Research. PEAT (Protein Engineering Analysis Tool) is not merely another laboratory information-management system (LIMS), but has been designed to address specific tasks encountered in a typical protein-engineering project while integrating data deposition in the process.

Vast amounts of data are generated yearly through the protein engineering methods used in the process of studying proteins. Although, these experimental data could be used in other research projects, there is no requirement to deposit it in a database before publishing and so it is unavailable for reanalysis or basically ‘lost' within the pages of a thesis or journal article.

Commenting on the benefits of PEAT, Dr Nielsen said, "The task of data capture and database deposition is frequently seen as a tedious and unrewarding process. PEAT incentivizes data storage by integrating the process with the analysis tools in a single application. I hope that researchers will see the benefits of using PEAT so that we can create and share high quality datasets on the connections between protein sequence, structure, and function.”

PEAT is written in the python programming language, and even though still under active development, has been evaluated on several projects within Dr. Nielsen's laboratory, and has been used to establish several online databases. Additional functionality specific to particular research projects can be implemented with specifically written plug-ins that allow users to customize the functionality of PEAT to specific experiments, proteins, or scientific questions.

Related Links:
University College Dublin Conway Institute