Proteomics Biomedicum

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.

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 strategies
  • 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.
  • 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 is available through iLab. 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. The customer would need to choose between the 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.

User fees

Fees for sample preparation for MS analysis, per sample
Sample preparation for MS analysis, per sample KI internal Academia Corporate
Protein extraction from harvested cells 100 150 200
Protein extraction from tissues 100 150 200
In‐gel alkylation, digestion 400 600 800
In‐solution alkylation, digestion 300 450 600
On-beads digestion 300 450 600
TMT labeling of one biological sample (TMT6plex, TMT10/11plex or TMTpro) 500 750 1000
Phosphopeptide enrichment on TiO2 300 450 600
Sample preparation for single cell proteomics (per 96-well plate) 5000 7500 10000
Off-line peptide fractionation 500 750 1000
Clean-up: Zip-tip, ion exchange column or membrane filter 100 150 200
Instrumental usage fees
Instrument time KI internal Academia Corporate
Orbitrap HF, per hour 500 750 1000
Orbitrap Fusion with ETD, per hour 550 825 1100
Orbitrap Lumos with ETD, per hour 600 900 1200
TMT-based single cell proteomics analysis, per experiment 2000 3000 4000
Accurate molecular mass determination (< 2 ppm) 1000 1500 2000
Fees for Bioinformatic analysis of MS data, per LC-MS run
Bioinformatic analysis of MS data, per LC-MS run KI internal Academia Corporate
Sequence database (e.g. Mascot) search 200 300 400
Label‐free quantification 200 300 400
TMT-labeling based quantification 200 300 400
Statistical analysis (per dataset of several LC/MS runs) 300 450 600
Fees for consultations, teaching, custom service, per hour
Consultations, teaching, custom service, per hour KI internal Academia Corporate
Custom MS or MS/MS data interpretation 400 600 800
Custom sample preparation/handling protocol 500 750 1000
Consultations before sample submission Free Free Free
Consultations after sample analysis PowerPoint slide preparation 400 600 800
Teaching, training 600 900 1200
Access to computers and software for data analysis 100 150 200
Release of original MS data, per datafile (LC/MS run – one file) Free Free 500

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) as indicated in the User fees above.

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, Wu C, van Hage M, Solovay K, Rubin K, Locht C, Thorstensson R, Thalen M, Loré K
J Clin Invest 2020 05;130(5):2332-2346

Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Petrus P, Lecoutre S, Dollet L, Wiel C, Sulen A, Gao H, Tavira B, Laurencikiene J, Rooyackers O, Checa A, Douagi I, Wheelock CE, Arner P, McCarthy M, Bergo MO, Edgar L, Choudhury RP, Aouadi M, Krook A, Rydén M
Cell Metab 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, Végvári Á, Smith ME, Qvarfordt I, Lindén A, Gräslund A, Agerberth B, Bergman P
Sci Rep 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, Safi F, Miharada N, Garcia SC, Siva K, Liu Y, Rörby E, Nilsson B, Zubarev RA, Karlsson S
Leukemia 2020 12;34(12):3323-3337

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, Végvári Á, Benfeitas R, Sperk M, Ståhlberg M, Krishnan S, Singh K, Penninger JM, Mirazimi A, Neogi U
Emerg Microbes Infect 2020 Dec;9(1):1748-1760

Content reviewer: