Dr. M. Niepel

Module B: Drug target identification and validation

• Basics of chromatographic separation and identification of small molecules • Basics of GC-MS and HPLC-MS • Understanding the role of computing in knowledge discovery and apply bioinformatics tools in data processing, workflow automation, and structure determination. • Ability to critically analyze and evaluate different approaches to generating models and simulations from biological databases. • Knowledge of the basic concepts of chromatography and mass spectrometry • Ability to set up a proteomics workflow in industry • Ability to judge the quality of results, i.e. protein identifications

Course H.1: Detection of potential contaminations • Sample preparation from biological matrices • Plant product chromatography • How to quantify, if there is no (standard) compound • Distinction of similar compounds • Labeling and spiking of samples • Practical examples and problems
Course H.2: Structure analysis • Bioinformatics in large scale proteomics and lipidomics • Genome and proteome databases, annotations, and search engines • Preprocessing of mass spectra • Principles and algorithms for peptide and protein sequence analysis • Identification of PTMs: classic and blind mode • Determination of elemental compositions by mass spectrometry • Molecular profiling and imaging techniques, Ion Mobility Spectroscopy • Vibrational spectroscopy: FT-IR, NIR, Raman, and Terahertz spectroscopies • Multivariate analysis for qualitative (principal component analysis) and quantitative (partial least squares regression) analysis
Course H.3: Protein analysis by mass spectrometry • Methods for separating complex protein and peptide mixtures (gel electrophoresis, HPLC) • In-gel and in-solution proteolysis of proteins • Protein mass spectrometry (ionization methods ESI and MALDI; mass analyzers TOF, LIT, , Orbitrap, hybrid instruments) • Peptide sequencing by mass spectrometry (MS/MS) • Database searches (Mascot) • Scoring algorithms for protein identification • Automation of the proteomics workflow

attestation on lab course contents - Course H.2: Structure analysis, attestation on lab course contents - Course H.3: Protein analysis by mass spectrometry, Protocol on lab course

Klausur