Advanced Mass Spectrometry Proteomics

Regional facility of national interest

The Advanced Mass Spectrometry Proteomics facility (AMSP) provide services using the best available proteomics techniques and methods not offered by any other facility in Sweden.


  • Blood profiling. Protein abundances and PTM:s.
  • PTM analysis. Unbiased PTM analysis at proteome level, of proteins and “silent” PTM:s, like isomerization.
  • Sequencing. de novo sequencing of polypeptides.
  • Quantitative proteomics. Protein identification and quantitation in complex biological samples.


  • Large scale quantitative proteomics experiment.
  • Accurate molecular mass determination of e.g. small molecules or peptides.
  • Detection of posttranslational modification and localization on amino acid sequence.
  • General protein identification and quantitation.


  • Chip-based electrospray ionization source. TriVersa NanoMate, Advion Metabolomics.
  • High pressure nano flow liquid chromatographic pump. UltiMate 3000 Nano LC System, Thermo Scientific.
  • High pressure nano flow liquid chromatographic pump. nEasy-LC 1000, Thermo Fisher.
  • High-resolution, accurate-mass Orbitrap mass spectrometer. Orbitrap Fusion, ThermoScientific.
  • High-resolution, accurate-mass Orbitrap mass spectrometers. Q Exactive and QExactive Plus, Thermo Scientific.
  • Ultra high pressure liquid chromatography system. UltiMate 3000 LC System, Thermo Scientific.
  • Triple Quadrupole mass spectrometer, Xevo TQ-S. Waters
  • Orbitrap Velos Pro hybrid ion trap-Orbitrap mass spectrometer. Thermo Fisher.


Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells. Aranda S et al., Nucleic Acids Res. 2014;42(11):6972-86. Epub 2014 May 22.

Binding of Pro-Gly-Pro at the active site of leukotriene A4 hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor. Stsiapanava A et al. ,Proc Natl Acad Sci U S A. 2014 Mar 3.

Prognostic Polypeptide Blood Plasma Biomarkers of Alzheimer's Disease Progression. Yang H et al. J Alzheimers Dis. 2014 Feb 6

Protein biomarkers in vernix with potential to predict the development of atopic eczema in early childhood. Holm T, et al. Allergy. 2014 Jan

Blood plasma IgG Fc glycans are significantly altered in Alzheimer's disease and progressive mild cognitive impairment. Lundström SL et al. J Alzheimers Dis. 2014

Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography. Kalantari S, et al. PLoS One. 2013 Dec

Wobble decoding by the Escherichia coli selenocysteine insertion machinery. [Xu et al., Nucleic Acids Res. 2013 Aug 27. PMID: 23982514].

In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models. [Lyutvinskiy et al., Mol Cell Proteomics. 2013 Aug;12(8):2324-31. doi: 10.1074/mcp.O112.023804. PMID: 23589346].