Bioinformatics to improve shotgun proteomics analyses. Towards an efficient Maldi-MS pipeline

PhD ceremony: Mr. T.P. Gandhi, 13.15 uur, Doopsgezinde Kerk, Oude Boteringestraat 33, Groningen

Dissertation: Bioinformatics to improve shotgun proteomics analyses. Towards an efficient Maldi-MS pipeline

Promotor(s): prof. B. Poolman, prof. R. Breitling

Faculty: Mathematics and Natural Sciences

Proteins play an overwhelmingly dominant role in living organisms as the work-horses of cells. The term proteomics, coined to serve as an analogy to genomics, is often defined as the comprehensive, quantitative study of protein expression and its changes under the influence of biological perturbations. The goal of a typical proteomics experiment is to juxtapose the set of expressed proteins from a living organism under different conditions such as temperature, mutation, nutrient availability, disease vs. healthy. The idea is to understand a biological system by looking at the differences between two or more states, in case of proteomics in the content, state (qualitative), and levels (quantitative) of proteins. Obviously, before any thorough quantitative analysis of differences can be undertaken, unknown proteins expressed in a biological sample must first be identified. Shotgun proteomics is an indispensible tool in high-throughput analysis of proteins in complex biological samples. Accurate peptide identification from liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) forms the cornerstone of such analyses. The work done in this thesis is related to the improvement in the performance of an LC-MALDI-based proteomics pipeline by focusing on several of its components, the outcome of which has resulted into several new algorithms and software solutions.