E! 6875 APB-platform Denator

Purpose and goal

Disease-specific enzymatic degradation of proteins was studied in patient samples with Barrett´s syndrome in various stages. Degradation was mapped using Stabilizor system & mass spectrometry and identified peptides was used to differentiate between disease stages. Synthetic peptides with disease-specific degradation sites were added to samples & aliquots analyzed repetitively to generate controlled degradation profiles. A large number of fragments were formed with different profiles. More work is needed to use these profiles to accurately determine disease stage.

Results and expected effects

Within the project we have developed a system based on the Stabilizor system, synthetic peptides and mass spectrometric analysis to study disease-specific protein degradation patterns. A number of peptides with Barrett´s syndrome-related cleavage sites have been synthesized and tested in extracts from clinical samples. The temporal degradation profile of peptides were analyzed and used to tentatively classify clinical samples. However, the predictive power of the classification was weak.

Approach and implementation

The project has been divided into a total of 10 WPs where many have been executed sequentially. A number of WPs have required several iterations of prototypes and methods in order for them to mature and function satisfactorily. With the extension of 6 months granted to the project it became possible to verify the whole system concept using synthetic peptides, the new thermal stabilization systems and using clinical samples. It can be concluded that the concept has been proof-of-concept tested but further work is needed to ensure that the whole system works reproducible as intended.