Mass Spectrometry-based Proteomics, Uppsala

Regional facility of national interest

The facility is located at the Biomedical Center in Uppsala. The facility offers expertise in sampling, sample preparation (e.g. selective extraction, affinity purification, depletion of abundant proteins), separation and fractionation (e.g. 1-D SDS-PAGE, liquid chromatography and capillary electrophoresis), mass spectrometry and general protein and peptide chemistry. The laboratory is equipped with several modern mass spectrometers, allowing for accurate mass determination and sensitive analyses of proteins, peptides and proteomes. Some recognized strengths of the facility are body fluid proteomics, tissue proteomics, phosphoproteomics, non-human proteomics and in-depth protein characterization.


  • Body fluid proteomics. E.g. cerebrospinal fluid and plasma.
  • Characterization of post-translational modifications. e.g. protein phosphorylation and glycosylation.
  • Determination of the intact mass of recombinant and native proteins.
  • Immunoprecipitation and identification of target proteins. The facility offers advice on experimental set up for identification of immunoprecipitated and co-immunoprecipitated proteins with MS.
  • In depth characterization of native and recombinant proteins.
  • Protein extraction. Selective extraction of proteins from cells and tissues.
  • Protein identification. From solution and gel spots/bands, quality control.
  • Protein separation. 1-D SDS-PAGE Ion chromatography fractionation (SCX, ERLIC)
  • Proteomics of samples from non-human species. E.g. cats, dogs, plants, bacteria and parasites.
  • Qualitative proteomics. Identification of proteins in complex biological samples.
  • Quantitative proteomics. Label-free and labeling techniques.
  • Training services. We provide courses and workshops.



  • Characterization of truncated and modified proteins, elucidation of enzymatic cleavage sites.
  • In-depth cerebrospinal fluid proteome analyses and determination of biomarkers for various disease states.
  • Simultaneous extraction of membrane bound and cytosolic proteins from cells and tissues, followed by MS-analysis.
  • Comprehensive characterization of phosphoproteins and phosphoproteomes.
  • Population-based Omics: Correlation of genomic data to MS-based proteomics results.


  • LTQ Orbitrap Velos Pro ETD MS. (Thermo Scientific).
  • QExactive Plus Orbitrap MS. (Thermo Scientific)
  • MALDI TOF/TOF MS. (Bruker Daltonics), 2 instruments.
  • 7T LTQ FTICR MS. (Thermo Scientific).
  • ESI-TOF MS. (Agilent Technologies).
  • Q-STAR XL. (Sciex).
  • Q-TRAP 3200. (Sciex).


Mehdi S, Derkacheva M, Ramström M, Kralemann L, Bergquist J, and Hennig L (2016) The WD40 Domain Protein MSI1 Functions in a Histone Deacetylase Complex to Fine-Tune Abscisic Acid Signaling. Plant Cell 28, 42-54.

Källsten M, Bergquist J, Zhao, H, Konzer A, Bergström Lind S. (2016) A comparative study of phosphopeptide-selective techniques for a sub-proteome of a complex biological sample. Anal Bioanal Chem, 408, 2347-2356.

Jansson R, Lau CH, Ishida T, Ramström M, Sandgren M, Hedhammar M. (2016) Functionalized silk assembled from a recombinant spider silk fusion protein (Z-4RepCT) produced in the methylotrophic yeast Pichia pastoris. Biotechnol. J. 2016 11

Undin T, Dahlin A, Hörnaeus K, Bergquist J, Bergström Lind S. (2016) Mechanistic investigation of the on-surface enzymatic digestion (oSED) protein adsorption detection method using targeted mass spectrometry. Analyst, 141, 1714-20

Goenaga J, Yamane T, Rönn J and Arnqvist G. (2015) Within-species divergence in the seminal fluid proteome and its effect on male and female reproduction in a beetle. BMC Evolutionary Biology 15:266

Knopp M, Andersson D I. (2015) Amelioration of the Fitness Costs of Antibiotic Resistance Due To Reduced Outer Membrane Permeability by Upregulation of Alternative Porins. Mol. Biol. Evol. 32:3252–63

Sundberg M, Bergquist J, Ramström M.(2015) High-abundant protein depletion strategies applied on dog cerebrospinal fluid and evaluated by high-resolution mass spectrometry. Biochemistry and Biophysics Report, 1, 68-75.

Eriksson O, Ramström M, Hörnaeus K, Bergquist J, Mokhtari D, Siegbahn A. (2014) The Eph tyrosine kinase receptors EphB2 and EphA2 are novel proteolytic substrates of tissue factor/coagulation factor VIIa. J Biol Chem. 289, 32379-91

Bergman JM, Wrande M, Hughes D. (2014) Acetate availability and utilization supports the growth of mutant sub-populations on aging bacterial colonies. PLoS One. 9(10):e109255

Sandh G, Ramström M, Stensjö K. (2014) Analysis of the early heterocyst Cys-proteome in the multicellular cyanobacterium Nostoc punctiforme reveals novel insights into the division of labor within diazotrophic filaments. BMC Genomics. 15:1064

Johansson, A., Enroth, S., Palmblad, M., Deelder, A. M., Bergquist, J., and Gyllensten, U. (2013) Identification of genetic variants influencing the human plasma proteome. Proc Natl Acad Sci U S A 110, 4673-4678

Jerlstrom-Hultqvist, J., Einarsson, E., Xu, F., Hjort, K., Ek, B., Steinhauf, D., Hultenby, K., Bergquist, J., Andersson, J. O., and Svard, S. G. (2013) Hydrogenosomes in the diplomonad Spironucleus salmonicida. Nat Commun 4, 2493