Core Facility


Clinical Proteomics Mass Spectrometry


Clinical Proteomics Mass Spectrometry (MS) is a core facility that offers you an opportunity to analyze the proteome composition of biological samples. The facility provides expertise and services in MS-based proteomics with focus on in-depth quantitative proteomics and proteogenomics. The facility also offers expert support in data analysis including multivariate feature selection, splice variant analysis at protein level and discriminant protein biomarker panel selection. We continuously strive to develop and implement cutting edge research methods in our services. This is exemplified by the level of data generated by the HiRIEF method used for in-depth proteomics, and by our bioinformatics methods for quantitative proteomics data, protein splice variant analysis and proteogenomics.



  • Experimental planning.
  • In-depth comprehensive proteome analysis.
  • Quantitative proteomics.
  • Proteogenomics. Annotation of protein coding DNA sequence.
  • Proteomics data analysis.


  • 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
    • High resolution Q-TOF 6540, Agilent.
    • LC-Triple Q-MS 6410, Agilent.
    • LC-Triple Q-MS 6490, with iFUNNEL system, Agilent.
  • Peptide separation technologies.
    • HiRIEF (High resolution isoelectric focusing)
    • Liquid Chromatography (UPLC/HPLC/FPLC).


  • In-depth proteome analysis of up to 10000 gene products.
  • Quantitative proteomics. Relative quantification between up to 10 different biological samples in one single experiment (isobaric labeling, isotopic labeling).
  • Identification of novel protein coding sequences in any organism with known DNA.
  • Targeted proteomics. Absolute quantification of proteins and peptides in biological samples.
  • Protein interaction studies.
  • Protein post translational modification analysis.


  • Ultrafiltration with size-exclusion liquid chromatography for high yield isolation of extracellular vesicles preserving intact biophysical and functional properties. Nordin JZ et al. Nanomedicine 2015
  • Multi-omic data analysis and systems biology using Galaxy. Boekel J. et al. Nature Biotechnol. 2015
  • SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data. Zhu Y., et al. Mol Cell. Proteomics. 2014
  • Development and application of a novel method for unbiased genome wide proteogenomics and the identification of multiple novel protein-coding loci in human and in mouse. Branca RMM et al. Nature Methods. 2013.
  • Direct observation of structurally encoded metal discrimination and ether bond (tyrosine-valine crosslink) formation in a heterodinuclear metalloprotein. Griese JJ et al. PNAS 2013.
  • Identification of a novel Organellar Oligo Peptidase (OOP) that provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts. Kmiec B et al. PNAS 2013.
  • Identification of retinoic acid receptor alpha as a novel predictive marker for tamoxifen treatment in breast cancer patients. Johansson HJ et al. Nature Commun. 2013.


If interested in our service please send an email to including a brief description of your request.

We will contact you within a few days.

        The facility will be closed for summer holidays between June 26th - August 14th.





Lukas Orre

Janne Lehtiö



Facility Director:

Prof. Janne Lehtiö, PhD

Head of Facility:

Lukas Orre, PhD

Research engineers:

Hillevi Andesson-Sand, MSc

Ghazaleh Assadi, PhD

Georgios Mermelekas, PhD

Lingjie Tao, MSc


Rui Branca, PhD

Rozbeh Jafari, PhD

Henrik Johansson, PhD

Maria Pernemalm, PhD


Mattias Vesterlund, PhD

Scientific programmer:

Jorrit Boekel, PhD


Alejandro Fernandez Woodbridge, PhD

Scientific coordinator:

Helena Bäckvall, PhD



Sample submission form

Price List


MS facility workflow