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Database Enrichment For Biomarker Discovery

(Literature Research Project at Analytical Biosciences)

Aim

We would like to know which molecules should be measured in supplementary mass spectrometry experiments in order to facilitate the discovery of new biomarkers?

Background

We have different ongoing mass spectrometry research projects where we need to identify new biomarkers. Biomarkers can be indicators of disease, or discriminate between two groups of patients.

We have built a database of experimentally acquired mass spectrometry data of human and plant metabolites. From our experiments we obtain spectra of biomarkers, which we need to identify. Their spectra are compared to this database. In the cases when the database is not helping, we can experimentally measure new known compounds to enrich the database and redo the comparison with our biomarker of interest. We expect these new data to contribute to the discovery of new biomarkers.

Your Task

Perform a literature research on the possible computational and experimental tools that can be used to select interesting molecules to add to our experiments.  Write a report on the state of the art and provide recommendations on how to implement the database enrichment.

This project can be extended to a full MSc thesis project involving real computational and laboratory research. We expect to you use the output of your project for our research.

Keywords

biomarker discovery, multi-stage mass spectrometry, computational research, molecular databases

Contact

Julio Peironcely:                   peironcely #at# chem.leidenuniv.nl

Peter Lindenburg:                 p.lindenburg #at# chem.leidenuniv.nl