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Instruments and Software used at the Proteomics Resource Center

The Proteomics Resource Center are equipped with a variety of LC and MS systems, including GC-MS and MALDI, and also houses peptide synthesizers.

  • Fusion Lumos w/APD. The Fusion Lumos was sponsored by the Sohn Conference Foundation. The instrument is connected to a 1200 Easy LC operating in nano-flow and the setup is currently dedicated to proteomics. The Fusion Lumos allows for CID, HCD and ETD as well as MSn fragmentation experiments.
  • Q-Exactive HF (donated by the Helmsley Foundation) is operated in nano-flow (Dionex 3000) and is also dedicated to proteomics.
  • Orbitrap XL is dedicated to higher flow LC and the analysis of small molecules, metabolites, nucleosides or for example when high mass accuracy and/or MS/MS is needed for molecules and larger amounts are available.
  • Q-Exactive Plus operated in higher uL-flow-mode (Vanquish HPLC) and is dedicated to metabolomics.
  • Our Vantage triple quadrupole is operated in high flow and used for example for MRM based analysis of nucleosides.
  • An LTQ linear ion trap is used for quality control of synthesized peptides.
  • MALDI (PerSeptive Biosystems DE-STR Voyager) is available as a walk-up user instrument.
  • GC-MS (Agilent 5977B Inert Plus MSD w/Intuvo 9000 GC).
  • Off-line LC based fractionation setup with UV or MS detection.
  • Typhoon 9400 Variable Mode Laser Scanner (click for usages fee and policy for use)
  • Symphony Peptide Synthesizer by Protein Technologies.
  • Intavis Multi-Pep Peptide Synthesizer by CEM.


Software’s: To answer the many types of questions that can be asked the Center operates many different software’s.

  • Proteome Discoverer – used together with MASCOT and/or SEQUEST and other node based tools.
  • Mascot – search algorithm (commercial)
  • Sequest– search algorithm (commercial)
  • MaxQuant – search algorithm with quantitation.
  • BYonic – search algorithm with quantitation (commercial)
  • PEAKSDenovo based search algorithm (commercial)
  • Skyline – for targeted analysis
  • Compound Discoverer – for data dependent metabolomics analysis (commercial)
  • Perseus – for data analysis