A three days workshop took place at the Center for Molecular Biology Heidelberg

First day:
Interaction Partners and Phosphorylated Peptides
Second day:
SILAC Data Analysis with MaxQuant / Perseus
Third day:
MRM with Skyline

Mass spectrometry (MS) is a high valuable tool in peptide and protein analysis. The increasing of instrument sensitivity and higher complexity of the data sets requires advanced knowledge in data handling and data interpretation. Deeper insights into the analysis of complex systems are getting more essential for life scientists in order to enable them a better evaluation and discussion of the data sets.

Dr. Thomas Ruppert, a group leader of the FOR2509 Research Unit and expert in mass spectrometry analysis, and Roman Sakson from the Core Facility for MS & Proteomics at the Center for Molecular Biology Heidelberg offered a workshop with hands-on training for the most commonly used methods in analysis of different kinds of proteomics datasets.

During the workshop, freely available academic software packages such as MaxQuant, Perseus or Skyline were introduced to the participants. During the first two days of the workshop the participants discussed the identification of interaction partners and of posttranslationally modified peptides as well as of regulated proteins using stable isotope labeling. At the last day the focus laid on relative and absolute quantification strategies as well as on targeted proteomics techniques. The workshop intensified the discussion between the participating doctoral students and postdocs about their „mass spec“ data sets of the FOR2509 Research Unit, so that they all had a great time together.


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