Stockholm University Proteomics Facility (SUPF) and the Analytical Chemistry Mass Spectrometry Facility

Stockholm University Proteomics Facility (SUPF) and the Analytical Chemistry Mass Spectrometry Facility

The facilities perform service regarding the sequencing of proteins and mass spectrometry of both small molecules and biomolecules.


The research projects in the Mass Spectrometry (MS) facility at the Analytical Chemistry department involve methods for both biomolecules and smaller molecules, e.g. pharmaceuticals or environmentally hazardous compounds. The facility has a subdivision, the Stockholm University Proteomics Facility (SUPF), which performs mass spectrometric sequencing of proteins.

SUPF is a co-operation between the Chemical and Biological Sections at Stockholm University, involving the departments of Analytical Chemistry, Biochemistry and Biophysics, Botany, Genetics, Microbiology, Molecular Biology, the Institute of Applied Environmental Research (ITM) and the Wenner-Gren Institute for Experimental Biology and Cell Research. Researchers from other departments and universities are also welcome to use the facility. Depending on your needs, we provide the infrastructure of the facilities or full service of your experiments. We provide high quality results and result analysis.


The Analytical Chemistry Mass Spectrometry Facility is located in building B2 the Arrhenius Laboratory for Natural Sciences. The facility consists of four MS-labs with operator rooms and a prep-lab accommodated in approximately 300 m2. At the present time the MS facility holds eleven mass spectrometers. There are GC/MS instruments with single and triple quadrupoles and one with an ion trap analyzer. Our LC/MS instruments include triple quadrupoles, ion traps and a q-ToF.

The Stockholm University Proteomics Facility is situated in one of the MS-labs and contains two main instruments: a MALDI-ToF and a q-ToF instrument. There is also a sample preparation workstation with centrifuges, a SpeedVac, refrigerators et c, so that the MALDI sample holder plates can be prepared on-site. The MALDI-ToF is an Applied Biosystems Voyager-DE STR. It is a fully equipped instrument with 15,000 resolution, reflectron, post source decay, timed ion gate and gas cell. This instrument is readily learned and operated. Being a part of the SUPF, the instrument is run by over 40 licensed operators (researchers as well as PhD students) from the chemistry and biology departments. The instrument also is used in education at advanced analytical chemistry, and at courses for professionally experienced analytical chemists.

Micromass q-ToF LC/MS is an atmospheric pressure ionization (API) system equipped for both electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI). The instrument is equipped with both a standard and nanospray interface for HPLC. The HPLC is an Agilent capillary-LC. In MS-only mode an orthogonal time-of-flight analyzer and a reflectron altogether provide for a mass range of 20,000 for singly charged ions and capability for exact mass measurement. In MS/MS mode ion selection and collision occur in a quadrupole analyzer and an rf-only quadrupole, respectively, before the ions enter the time-of-flight analyzer.

Practical information

The researchers that want to perform the experiments themselves have to obtain a certificate showing that they have sufficient skills to run each instrument. Contact us for more information.

If you want full service, please contact us in order to discuss the experiments.

Priority is given to the research projects within the own departments, although there is usually room for external users. The experiments are usually completed within a week, although this depends on the particular project.

Prices are open for negotiation; please contact us for more information. For customers from academic institutions, the identification or quantification of small molecules normally costs 500 SEK/hour, but at minimum 2 500 SEK per sample. This price includes results analysis. For customers from commercial institutions, the corresponding charges are 1 000 SEK and 5 000 SEK, respectively.

We offer courses in mass spectrometry.

Interested in Industry collaboration
Arrhenius Laboratory of Natural Sciences
Stockholm University
106 Stockholm
+46 (0)8 674 71 97