Chemical Proteomics & Proteogenomics

National facility

Chemical Proteomics & Proteogenomics is a national facility that offers state-of-the art mass spectrometry based proteomics support to the Swedish research community. The facility also offers expert support in experimental planning, MS-analysis and data analysis related to proteogenomics and chemical proteomics. The activities are shared between two sites in Stockholm: one at SciLifeLab and one at Karolinska Institutet. The chemical proteomics and proteogenomics facility is also a node in Swedish National Mass Spectrometry Facility BioMS, more information see bioms.se

Proteogenomics in brief
Proteogenomics is a new exciting field in biological mass spectrometry that combines proteomics information with sample specific genomic and transcriptomics information. Applications in proteogenomics include discovery of novel protein coding regions to improve genome annotation; detection of variant and mutated proteins based on DNA and/or RNA sequence data; discovery of cancer neoantigens and evaluation of the impact of genomic changes (e.g. copy number alterations, SNPs, mutations, hyper methylation) on the proteome. We can also provide in-depth proteomics data for comprehensive systems biology studies.

Chemical Proteomics in brief
Chemical proteomics includes a powerful set of complementary, mass spectrometry based and proteome-wide approaches to identifying key proteins relevant for producing the phenotypic effects of a treatment. Chemical proteomics includes affinity capture approaches using compounds as bait to study interacting proteins. Thermal profiling exploits the fact that protein denaturation temperatures can be affected, both positively and negatively, when the system is perturbed with a chemical compound. Proteome-wide mapping of these thermal changes helps to understand the mechanisms of molecular changes induced in the cell by the chemical compound. To decipher the key proteins in the mechanism of action, quantitative proteomics can also be utilized by evaluating the specific regulation of certain proteins due to a certain treatment. This can be achieved using a specifically designed multiple compounds approach, also known as FITExP (functional identification of targets by expression proteomics). Moreover, the binding site of a chemical compound to a particular protein can be probed by deuterium exchange experiments using mass spectrometry (MS).


  • Unbiased proteogenomics in any species with a sequenced genome
    Six frame translation of genome generated database searches for protein coding genome annotation.
  • Personalized proteomics
    Individual sequence based search database generation for variant analysis at the protein level coupled with in-depth quantitative proteome analysis.
  • Disease state/Variant proteomics
    Database supplemented with all known SNPs and disease causing genetic alterations. (Can be used when sample specific sequence data is not available.)
  • XenoProteomics
    Database supplemented with peptides from disease causing pathogens.
  • Affinity capture using click chemistry based probes followed by MS analysis in collaboration with national drug development and chemical biology infrastructures (who can help with the organic synthesis of needed affinity probes).
  • Key protein engagement studies. Kinetic profiling post compound exposure
  • Thermal profiling proteomics. Proteome-wide mapping of changes in thermal stability of proteins after chemical perturbation using quantitative proteomics.
  • Identification of key proteins and Mechanism of Action Identification by specifically designed quantitative proteomics using the multiple drugs/compounds FITExP method
  • Key protein characterization by top-down proteomics
  • Interaction interface elucidation by hydrogen-deuterium exchange MS


If you need support for other type of MS-based projects please visit the regional core facilities :

  • or view what other services are available via bioms.se


  • Mass spectrometers.
    • MS Orbitrap Q Exactive, Thermo Scientific.
    • MS Orbitrap HF Q Exactive, Thermo Scientific
    • MS Orbitrap Fusion, Thermo Scientific
    • MS LTQ Orbitrap Velos Pro, Thermo Scientific
    • MS LTQ Orbitrap Elite, Thermo Scientific
    • LC-Triple Q-MS 6490, with iFUNNEL system, Agilent.
  • Peptide separation technologies.
    • HiRIEF (High Resolution Isoelectric Focusing)
    • Liquid Chromatography (nanoUPLC/HPLC/FPLC)