Proteome Center Tuebingen

The core expertises of the Proteome Centre Tübingen (PCT) are in methods of protein analysis, such as different electrophoresis techniques and protein identification by mass spectrometry. PCT recently extended its expertise and shifted the emphasis to the workflows in the area of high accuracy peptide-based (“shot-gun”) quantitative proteomics that enable high dynamic range of protein detection. The quantitative workflows are mainly based on stable isotope labeling of cells and tissues and measurements of resulting protein digests using state-of-the-art LTQ-Orbitrap mass spectrometry. In addition, PCT possesses considerable infrastructure and expertise in protein/peptide separation technologies based on various analytical HPLC methods (strong cation exchange, reversed-phase chromatography, etc.), as well as bioinformatic analysis of shot-gun proteomics data. As a core facility of the University of Tuebingen, the Proteome Center Tuebingen (PCT) offers proteomic analyses against a fee to researchers in academia and industry alike. We offer various workflows for qualitative and quantitative analyses of proteins, proteomes and subproteomes (e.g. phosphoproteome, interactome). Other posttranslational modifications can also be analyzed upon request. Quantitative workflows are mainly based on stable isotope labeling of cells and tissues (SILAC); SILAC-labeling can be done either by the collaborators, or in our laboratory. Scientists that are still interested in performing 2D PAGE are invited to use the equipment in our laboratory.

Proteome biochemistry

• PAGE (1D, 2D, Blue Native) • Western blotting • GeLC-MS • Filter-aided sample preparation (FASP) • Phosphopeptide enrichment • Strong cation exchange chromatography (SCX) • TiO2 chromatography • Offgel peptide separation • SCX peptide separation • Stage-tip peptide purification

Liquid chromatography - Mass spectrometry

• NanoHPLC column packing • 2D HPLC (SCX+RP) • nanoHPLC-MS/MS (LTQ-Orbitrap XL) • nanoHPLC-MS/MS (Q-TRAP 4000)

IT/Bioinformatics

• Pipeline for Orbitrap data analysis (based on Mascot and MaxQuant) • Protein/Peptide identification • SILAC quantitation • Peptide modification analysis • Pipeline for Q-TRAP data analysis (based on Mascot and OpenMS) • Protein/Peptide identification • MRM quantitation • SILAC quantitation • Downstream analysis of shotgun proteomics data