Rune Matthiesen

We have established experimental sample processing pipelines for LC-MS analysis and developed several proteomics software pipelines for proteomics based on high throughput LC-MS. The unique feature of our software is that it can include many variable modifications (~40 have been tested) in a single search against the full protein database when searching state of art LC-MS data. We have also standardized the analysis of all main MS-based quantitative methods. This is a major breakthrough and we can demonstrate that current state of art MS is so sensitive that a large number of protein modifications can be found directly without tedious peptide enrichment for specific modifications. This technology will become even more significant as MS instruments get cheaper and more sensitive. We are currently working on commercializing this novel software tool for analysis of state of art LC-MS data. We will furthermore continue to use our sample preparation and software pipelines together with our collaborators in the COST action “PROTEOSTASIS” and pharmaceutical companies. We have for example previously had paid projects from GlaxoSmithKline, Novo Nordisk and Novartis. Finally, we established biobanks for OSA and COPD which we are currently exploring by next generation sequencing and high throughput LC-MS for biomarker discovery. We aim in these projects to provide complete diagnostic tools including Bayesian software to be commercially explored.