Ausstattung & Software

Ausstattung & Software

Proteomics platform

In detail, we provide the following state-of-the-art MS instrumentation and methods:

Mass spectrometry platforms:

  • Two Q-Exactive Plus coupled online to an Ultimate 3000 nanoLC-system (both from Thermo-Fisher Scientific) for discovery-driven workflows
  • MALDI-TOF/TOF (4800 ABI-SCIEX) for fast analysis of low complexity samples

Sample fractionation instruments:

  • 3100 OFFGEL Fractionator for peptide separation using isoelectric focusing (Agilent)
  • MALDI-Spotter (Suncollect)


  • Database search tools: Mascot, Sequest and Andromeda for peptide/protein identification
  • Scaffold (Proteome software) for exchanging proteomics results with clients
  • Progenesis QI label-free quantification software (Nonlinear Dynamics)
  • MaxQuant for quantification of isotopically labeled samples
  • Skyline for analysis for absolute protein protein quantification via labelled peptide standards

SafeQuant for absolute protein quantification and statistical analysis of quantitative datasets (developed at the Biozentrum Basel Proteomics Core Facility)


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