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 andproteogenomics facility is also a node in Swedish National Mass Spectrometry Facility BioMS, more information 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 makes use of mass spectrometry for identification of proteome-wide compound-target interactions. Chemical proteomics includes affinity capture approaches using drugs/compounds as bait to study interacting proteins. Interactions between proteins and drugs/compounds can also be identified by thermal profiling. Thermal profiling exploits the fact that protein denaturation temperature is shifted upon ligand binding. Proteome-wide probing is performed by temperature series of quantitative proteomics analyses. Proteomics can also be used to probe the proteome wide effects of a drug treatment in a quantitative proteomics experiment. Moreover, the binding site of a drug with a particular protein can be probed by deuterium exchange experiments using mass spectrometry.


  • 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.
  • Target discovery: Affinity capture using click chemistry based probes followed by MS-analysis, and thermal proteome profiling based target discovery (in collaboration with Chemical Biology Facility, LCBKI).
  • Target engagement studies. Kinetic profiling post compound exposure andthermal proteome profiling
  • Target characterization by top-down proteomics
  • Interaction interface elucidation by deuterium exchange mass spectrometry assays


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

  • Clinical Proteomics Mass Spectrometry (eg, in-depth proteome analysis, quantitative proteomics, plasma proteomics, etc). The facility is closed during summer holidays between June 26th - August 14th.
  • or view what other services are available via


  • 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)