Proteomics in Systems Biology

Dr. Joerg Reinders Institute of Functional Genomics University Regensburg Joseph-Engert-Strasse 9 93053 Regensburg Germany Phone: +49 941 943 5004 Fax: +49 941 943 5019 E-Mail: joerg.reinders@klinik.uni-regensburg.de

Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines.- ample Preparation Approaches for iTRAQ Labelling and Quantitative Proteomic Analyses in Systems Biology.- Two birds with One Stone: Parallel Quantification of Proteome and Phospho-Proteome Using iTRAQ.- Selected Reaction Monitoring to Measure Proteins of Interest in Complex Samples: A Practical Guide.- Monitoring PPARG Induced Changes in Glycolysis by Selected Reaction Monitoring Mass Spectrometry.- A Targeted MRM Approach for Tempo-Spatial Proteomics Analyses.- Targeted Phospho-Proteome Analysis Using Selected/Multiple Reaction Monitoring (SRM/MRM).- Testing Suitability of Cell Cultures for SILAC-Experiments Using SWATH-Mass Spectrometry.- Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes.- Tissue MALDI Mass Spectrometry Imaging (MALDI MSI) of Peptides.- Ethyl Esterification for MALDI-MS Analysis of Protein Glycosylation.- Characterization of Protein N-Glycosylation by Analysis of ZIC-HILIC-Enriched Intact Proteolytic Glycopeptides.- Simple and Effective Affinity Purification Procedures for Mass Spectrometry-Based Identification of Protein-Protein Interactions in Cell Signaling Pathways.- A Systems Approach to Understand Antigen Presentation and the Immune Response.- Profiling of Smal

l Molecules by Chemical Proteomics.- Generating Sample Specific Databases for Mass Spectrometry Based Proteomic Analysis by Using RNA Sequencing.- A Proteomic Workflow Using High Throughput De Novo Sequencing towards Complementation of Genome Information for Improved Comparative Crop Science.- From Phospho-Proteome to Modelling of Plant Signalling Pathways.- Interpretation of Quantitative Shotgun Proteomic Data.- A Simple Workflow for Large Scale Shotgun Glycoproteomics.- Systemic Analysis of Regulated Functional Networks.