Clinical proteomics - mass spectrometry facility

Clinical proteomics - mass spectrometry facility

The facility provides advanced analysis of proteins, peptides and metabolites using state-of-the-art molecular separation and mass spectrometry (MS) analysis technologies. The facility also functions as an educational and a resource center focusing on quantitative clinical proteomics. The MS-platform facility provides fee-for-service sample analysis as well as support to plan and perform larger in depth proteomics projects.


Clinical proteomics/mass spectrometry unit is operating as core facility and as a competence unit for MS-based proteomic analyses. The staff and researchers in the group are affiliated with several departments at the Karolinska Institutet as well as the Karolinska University Hospital, and have a high competence on various proteomics technologies. The platform is led by associate professor Janne Lehtiö. We work both on number of proteomics projects as well as in development of new methods for clinical "omics" research. The researchers are engaged in method development projects to improve tissue and plasma proteomics for example using peptide isoelectric focusing as a pre-fractionation method, improve post translational modification analysis, subcellular relocalisation analysis and targeted proteomics to increase sensitivity and throughput in clinical validation of proteomics data. Further, we use mass spectrometry based proteomics to discover new biomarkers and to understand proteome changes related to cancer and other diseases. We work in close collaboration with clinicians at the Karolinska University Hospital as well as other clinicians at other hospitals in Sweden. The analysis methods used are motivated by the clinical need of new diagnostic and prognostic tools, understanding the disease mechanisms as well as tools for prediction of therapy efficacy. Starting material in proteomics projects include cell line samples, tissues, plasma and other body fluids collected according to standard operation procedures. Part of the work is linked to materials collected in conjunction with clinical trials.

The clinical proteomics/mass spectrometry unit also hold courses on mass spectrometry and omics data analysis. Information on activities are posted site as well as around KI.


We focus on quantitative MS proteomics including study design, sample analysis and data analysis. The proteome quantitation is mainly achieved using isotopic labelling techniques (such as TMT & SILAC). The complex protein mixtures are separated prior MS analysis using one or multiple peptide separation step.

The mass spectrometry facility is equipped with the latest peptide separation techniques and mass spectrometry instrumentation including a suit of mass spectrometers with complementary characteristics including high resolution LC-ESI mass spectrometers for quantitative proteomics and post translational modification analysis (QExactive; High Field QE, Orbitrap Fusion, Orbitrap Velos), high resolution QTOF (Agilent), and  tripleQ instrumentation for targeted mass spectrometry analysis.

Assurance of quality

We are a research core facility and are not ISO or GLP certified.

Science for Life mass spectrometry platform is a continuation of the clinical proteomics facility at Karolinska University Hospital and has operated since 2005. The facility is working in connection to Professor Lehtiö's group with strong methodological research providing latest methods to the facility.

Practical information

Please visit our site for additional information.


Interested in Industry collaboration
+46 (0)8 524 81416