Proteomics Biomedicum

Proteomics Biomedicum is the proteomics core facility at MBB. The Proteomics Biomedicum facility provides services using best available mass spectrometry-based proteomics techniques and methods with focus on quantitative proteomics, including single cell proteomics. We help designing experiments, providing a broad range of efficient samples preparation methods, high quality mass spectrometric data as well as data analysis and interpretation.

About Proteomics Biomedicum

Proteomics Biomedicum (previously Proteomics Karolinska PK/KI) is the proteomics core facility at the Department of Medical Biochemistry and Biophysics located in the Biomedicum building. We provide a broad range of services using best available proteomics techniques and methods with focus on quantitative proteomics, both label-free and multiplexed TMT-labeling.

Based on our experiences accumulated in many years, we are always glad to discuss projects related to identification and quantification of proteins and assist with experimental design as well as to deliver high quality results.

We are proud to open the door of the facility and welcome few and single cell proteomic projects. We have recently established an experimental workflow that allows us to analyze extremely low amounts of proteins extracted from single cells and generate quantitative results with reasonable depth of the proteome.

Similarly, we are able now to work with low number of cells that has been a challenge earlier when samples were available in limited amounts.


  • Single cell proteomics by mass spectrometry
  • Large scale quantitative proteomics experiments using label-free or isobaric labeling (TMT and TMTpro) quantification stratedies
  • Targeted proteome analysis, including SureQuant analysis of plasma/serum samples
  • Accurate molecular mass determination of peptides and small proteins
  • Detection of posttranslational modification and their localization on the amino acid sequence
  • General protein identification in gel and solution


Instruments at the Proteomics Biomedicum core facility. Photo: N/A

Mass spectrometers: 

  • Orbitrap Lumos (Thermo Scientific) - High-resolution, high mass accuracy tribid mass spectrometer
  • Orbitrap Fusion (Thermo Scientific) - High-resolution, high mass accuracy tribid mass spectrometer
  • Q Exactive HF (Thermo Scientific) - High-resolution, high mass accuracy Orbitrap mass spectrometer
  • Q Exactive (Thermo Scientific) - High-resolution, high mass accuracy Orbitrap mass spectrometer

Liquid chromatography systems: 

  • UltiMate 3000 Nano LC System (Thermo Scientific) – Ultra high pressure, nano-flow liquid chromatography system
  • UltiMate 3000 LC off-line fractionation (Thermo Scientific) - High pressure nano-flow liquid chromatography systems

TriVersa NanoMate (Advion Metabolomics) - Chip-based electrospray ionization source

Operating Guidelines

The services of Proteomics Biomedicum will soon be available through iLab (mid November 2020) until then please, contact with us using information below. From October 1, 2020 the following guidelines are introduced:

After discussion but before submission of samples, the customer is kindly requested to provide a brief description of the project. Please use the template for the research description. The customer would need to choose (and/or) different levels of services:

  • Contract (service) analysis (Research data acquisition. No data analysis or interpretation will be provided by facility. Archiving and public access is customer’s responsibility. No intellectual property will be retained by the facility. No authorship demand by facility. User fee will be applied.)
  • Collaborative analysis (Besides research data acquisition (for which the same user fee will be applied as in Contract (service) analysis), data analysis and interpretation will be provided. Archiving and public access will be provided. Intellectual property will be shared & authorship will be shared (see Rules on Intellectual Property and Publications for details).

Proteomics Biomedicum is also happy to be engaged with Collaborative research, when the facility is part of the grant application together with collaborator(s) and develop new analytical methods applicable to collaborator’s analytical problem.

Access to LC-MS/MS instrumentation

It is now possible to get access to LC-MS/MS instrumentation for the qualified personnel of your groups, for the following service fee:

  • Start-up charge - 3,000 kr.

 Additionally, hourly charge per every booked consecutive hour (4 h minimum):

  • Q Exactive - 400 kr/h;
  • Q Exactive HF and HF X - 500 kr/h;
  • Fusion Tribrid with ETD - 550 kr/h;
  • Lumos Tribrid - 600 kr/h.

No IP will be retained by the core facility. The custody of the data files produced will be yours, with the obligation to archive them and eventually make publicly available according to the Swedish law and KI regulations. 

Visiting Address

Karolinska Institutet
Department of Medical Biochemistry and Biophysics (MBB)
Biomedicum, floor 9
Solnavägen 9
Stockholm, Sweden


If you are interested in using our services or you wish to discuss your project, please contact lab manager Akos Vegvari.

Akos Vegvari

Head of Facility


Recent Projects

Live attenuated pertussis vaccine BPZE1 induces a broad antibody response in humans.
Lin A, Apostolovic D, Jahnmatz M, Liang F, Ols S, Tecleab T, et al
2020 May;130(5):2332-2346Glutamine Links Obesity to Inflammation in Human White Adipose Tissue

Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Petrus P, Lecoutre S, Dollet L, Wiel C, Sulen A, Gao H, et al
2020 02;31(2):375-390.e11

Studies on citrullinated LL-37: detection in human airways, antibacterial effects and biophysical properties.
Al-Adwani S, Wallin C, Balhuizen MD, Veldhuizen EJA, Coorens M, Landreh M, et al
2020 02;10(1):2376

S100A6 is a critical regulator of hematopoietic stem cells.
Grahn THM, Niroula A, Végvári Á, Oburoglu L, Pertesi M, Warsi S, et al
2020 Jun;():

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.
Appelberg S, Gupta S, Svensson Akusjärvi S, Ambikan AT, Mikaeloff F, Saccon E, et al
2020 Dec;9(1):1748-1760