Electrospray Ionization tandem Mass Spectrometer with Ion Trap mass analyser and Nano Liquid Chromatography



amaZon Speed ETD

Room 612

Contact: K. Skowronek

Access: collaboration/contracted research, experienced users (internal)

General description

The setup consists of Proxeon nanoLC EasyII chromatography system with C-18 reverse phase nano-column and Bruker amaZon mass spectrometer equipped with CaptiveSpray nonoBooster ESI source with two modes of fragmentation (CID and ETD) and up to 20 Hz polarity switching capability.


  • This system is continuously used for proteomic analysis of samples from SDS-PAGE gels (assisting protein purification assessments).
  • MS/MS analysis of small homogeneous nucleic acids
  • Analysis of simple mixtures of small molecules

Protein identification (in gel band)

Analysis of tRNAPhe after T1 nuclease fragmentation

Other applications are always welcome but due to rather low mass resolution and sensitivity of this equipment results might be unsatisfactory in more demanding applications (analysis of complex mixtures of proteins and other compounds, quantitative MS analysis)

Sample requirements

Samples for protein identification (pieces of SDS-PAGE gels) are continuously collected in “MS” box in top drawer of the freezer in room 607A. Processing starts every Wednesday. Please send email stating the organism from which protein was purified. For recombinant proteins please indicate expression platform and send full amino acid sequence of a recombinant protein in a single letter format.

All other samples require prior consultation

Further reading

  1. Domon B, Aebersold R. Mass spectrometry and protein analysis. Science. (2006) 312(5771):212-7. Review. PubMed PMID: 16614208.
  2. Rappold BA. Mass Spectrometry Selectivity, Specifically. Clin Chem. (2016) 62(1):154-6. doi: 10.1373/clinchem.2015.240614. Epub 2015 Oct 1. PubMed PMID: 26430070.