An open-source framework for mass spectrometry and TOPP – The OpenMS Proteomics Pipeline

Fall User Meeting 2011

1.-2. Sept. 2011 @ Free University Berlin

This years fall user meeting included interesting talks, an OpenMS tutorial session and a group discussion for data management in mass spectrometry, rounded out with a small complimentary dinner.

Talks and Keynotes

We had some interesting talks from the OpenMS team and some of the participants.

  • Peptide Feature Detection and Quantitation in OpenMSLars Nilse
  • Metabolite Feature Finding, Erhan Kenar
  • Label-free quantification with OpenMS 1.8, Hendrik Weisser
  • Error Tolerant Search Strategies for Protein Identification, Bernhard Renard
  • Exhaustive Isotopic Multiplexing for Quantitative Proteomics, Marc Kirchner
  • Extensive Multi-Search Strategy Reveals Significant Increase in Identification Rates of Modified Peptides, Timo Sachsenberg
  • MSSimulator: Simulation of Mass Spectrometry DataStephan Aiche
  • Analysis of MS data from UV induced protein-RNA cross-linking experiments, Katherina Kramer
  • Statistical modelling and inference for MS data, Andreas Ipsen
  • iTRAQ Data Evaluation and Quality ControlChris Bauer

We also thank the two keynote speakers for their interesting contribution to the User Meeting.

  • Mass Spectrometry in Systems Biology – Data Management and Data Processing, Lars Malmström
  • PRIDE and ProteomeXchange – Data Deposition and Dissemination, Henning Hermjakob


  • Lars Malmström, ETH Zürich
  • Henning Hermjakob, European Bioinformatics Institute
  • Marcel Kwiatkowski, University Clinics Hamburg
  • Bernhard Renard, Robert Koch-Institute Berlin
  • Katharina Kramer, MPI Göttingen
  • Florian-Alexander Herbst, Helmholtz-Zentrum für Umweltforschung
  • Christian Schiffmann, Helmholtz-Zentrum für Umweltforschung
  • Andreas Ipsen, Berlin Institute for Medical Systems Biology
  • Lisa Weilnböck, Uni Salzburg
  • Eryk Wolski, Bruker Daltonics
  • Silke Ruzek, Uni Salzburg
  • Chris Bauer, Microdiscovery Berlin
  • Marcel Blindert, Research Unit Protein Science / Helmholtz München
  • Hendrik Weisser, ETH Zürich
  • Marc Kirchner, Harvard Childrens Hospital
  • Hannes Roest, ETH Zürich
  • Christoph Dieterich, MDC for Molecular Medicine Berlin