Computational methods in high throughput MS-based proteomics

ITQB Seminar

Title: Computational methods in high throughput MS-based proteomics

Speaker: Rune Matthiesen

Affiliation: IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto

Host: Cláudio M. Gomes- Head of Prot. Biochemistry Folding and Stability Laboratory

Abstract:

Surely, DNA based technologies outperform proteomics in terms of throughput and cost effectiveness. A more relevant question is whether DNA based technologies gives us the important answers. I will based on this question provide some motivating examples to why high throughput proteomics deserves more attention.

We have in our group established a complete pipeline for high throughput proteomics. We have mainly focused on clinical proteomics for defining biomarkers but the pipeline can in principle be used in any biological project. The main novelty of our pipeline compared to existing pipelines is that we can search the complete sequence database with many variable modifications. We are able to perform such searches with large scale data in a timely manner without inflating the false positive rate by using a novel procedure.

In summary, the audience will be familiarized with how peptides and proteins are identified and quantified based on high throughput MS-based proteomics. Furthermore, a small number of case studies from previous and current projects, mainly in the area of clinical proteomics, will be discussed to illustrate a few of the many possibilities that MS has to offer.