National facility

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.


  • 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.)
  • Unbiased proteogenomics in any species with a sequenced genome
    Six frame translation of genome generated database searches for protein coding genome annotation.
  • XenoProteomics
    Database supplemented with peptides from disease causing pathogens.
  • Meta proteomics
    Proteogenomics analysis based on metagenomics database generation
  • Plasma proteomics
    In-depth global MS-based plasma proteomics


If you need support for other type of MS-based projects please visit our regional core facility : Clinical Proteomics Mass Spectrometry (eg, in-depth proteome analysis, quantitative proteomics, IP-MS, etc) or view what other biological MS based services are available via bioms.se


  • Mass spectrometers .
    • Q Exactive HF (4), ThermoFisher
    • Q Exactive (1), ThermoFisher
    • timsTOF Pro (1), Bruker
  • Peptide separation technologies.
    • HiRIEF (High Resolution Isoelectric Focusing)
    • Liquid Chromatography (nanoUPLC/HPLC/FPLC) Dionex, Agilent
  • Robots
    • Ettan Digester (modified Gilson 215), GE Healthcare Life Science
    • Pi-pet Sampleprep (modified Tecan Xantus), LAT