Chemical Proteomics Core Facility

Our facility is specialized in supporting target identification and validation, keys and bottlenecks of drug discovery and development. 

What we offer

Our facility is specialized on the identification and characterization of proteins primarily involved in drug responses, by means of drug targets and/or mechanism of actions.

We can tailor our service on specific scientific goal(s) in the area of chemical proteomics, by providing and combining different methods.

Our current focus is unbiased mass spectrometry-based and proteome-wide approaches to probe the effects of small molecules, e.g. drugs compounds, on cells and organisms, as well as the properties of proteins using small molecules as probes. Through these methods we can identify primary and secondary drug targets in cells and tissues with no need of chemical modification of the compound.

Unbiased proteomics methods:

  • FITExP (Functional Identification of Target by Expression Proteomics), recently invented in our laboratory, which enables to reveal target and mechanism of action proteins by studying the specific regulation of the proteome in response to a certain compound, e.g. the response of mammalian cancer cells to an anticancer drug.
  • TPP (Thermal Proteome Profiling), which enables the identification of the drug binding proteins by measuring compound-induced variations in thermal stability of proteins at the level of the whole proteome.

The combined application of FITExP and TPP provides unprecedented insight into the drug-target interaction.

Other services:

  • Mass-spectrometry based proteomics for identification of compound-target interactions after affinity capture approaches
  • Determination of the compound-protein binding site by hydrogen-deuterium exchange mass spectrometry (HDX MS).

Our services can include

  • Consultation and experiment planning
  • Cell culture and drug / compound treatments
  • Cells / tissue sample processing, MS-based proteomics and identification of compounds-target(s) interactions and/or mechanism(s) of action
  • Elucidation of interaction interface using hydrogen/deuterium exchange mass spectrometry
  • MS-analysis and complete data analysis of results
  • Functional data analysis and interpretation
  • Tables and figures of final data

Study aims we can help you with

  • Target Identification
  • Discovery of Mechanism of Action
  • Elucidation of Interaction Binding Site
  • Change in Redox State
  • Mechanism of Cell Death

Our equipment

Mass spectrometers:

  • MS Orbitrap Q Exactive HF, Thermo Scientific
  • MS Orbitrap Q Exactive Plus, Thermo Scientific
  • MS Orbitrap Q Exactive, Thermo Scientific.
  • MS Orbitrap Fusion, Thermo Scientific
  • MS LTQ Orbitrap Elite, Thermo Scientific

Peptide separation technologies:

  • HiRIEF (High Resolution Isoelectric Focusing)
  • Liquid Chromatography (nanoUPLC/HPLC/FPLC)

How to book our service

Please feel free to contact us or come visit us to receive help and find out about feasibility and details for your project. We can customize and tailor our services on your specific case.

The Chemical Proteomics Core Facility is part of the national infrastructure for biological mass spectrometry BioMS. We can support your project and cover relevant costs of it by national funding.

Please submit your project request via the BioMS portal:

  • Please tick "Chemical proteomics” in the application
  • In the field BioMS contact, please specify: “Zubarev/Gaetani” 


Head of facility

Massimiliano Gaetani

Organizational unit: Roman Zubarev's group

Visiting address



Karolinska Institutet
Department of Medical Biochemistry and Biophysics (MBB)
Biomedicum, A9, floor 9
Solnavägen 9
171 65 Solna

The Chemical Proteomics Core Facility at Karolinska Institutet is located at the Department of Medical Biochemistry and Biophysics (MBB). Together with the Proteogenomics facility at SciLifeLab, we constitute the Chemical Proteomics & Proteogenomics facility, which is the Stockholm node of BioMS, the Swedish national infrastructure for biological mass spectrometry. We are part of the Division of Physiological Chemistry I, headed by Roman Zubarev.


Core facilityProteomics