BioMediTech Research Infrastructure

Mass Spectrometry Facility

Facility offers analysis services based on mass spectrometry technique. Services include clinical proteomic analyses and we have capacities to analyse samples with state of the art NanoLC-MSTOF and MicroLC-MSTrap equipments.


NanoLC-MSTOF liquid chromatography-mass spectrometry is an analytical technique, which first separates compounds based on their chemical properties according to a gradient flow, and then ionizes the chemical compounds and identifies them based on mass-to-charge ratio and fragmentation patterns.

Our facility has specialized in label-free relative quantitation of proteins from small clinical samples using SWATH-MS method. The facility has broad proteomics capabilities offering analysis for small and large-scale studies, including basic protein identification studies as well as clinical trials/discovery studies. Facility can provide full service with sample preparation, analysis and bioinformatics if needed.

Typical protein discovery study includes SWATH-MS relative quantitation library creation, sample preparation, SWATH-MS analysis, relative quantitation of results and bioinformatics. Typical study using tissue samples or cell lysates with relatively simple sample handling yields 3000-4000 relatively quantified proteins per sample.

Possible samples include e.g.

  • Body fluid (tear, blood, plasma, urine etc.)
  • Tissue (fresh or paraffin-embedded)
  • Cell lysate
  • Cell culture medium
  • Extracellular vesicles
  • Pull-down mixture
  • Protein band from SDS-PAGE gel

We can also provide additional confirmation/validation analyses using MicroLC-MSTrap equipment for known targets.

We have established multiple quantification libraries. Please enquire if we already have library, which suits your needs.

Please fill out our inquiry form (pdf) and we are happy to discuss your needs further!


All the users of the Mass Spectrometry Facility services are obligated to acknowledge the facility in publications:

“The authors acknowledge the Tampere Mass Spectrometry Facility for their service.”


Sample preparation equipment include Thermomixers, spectrophotometer, miVac sample concentrator and HPLC-UV with fraction collection.

Facility has NanoLC-MSTOF instrumentation using Eksigent 425 NanoLC coupled with Sciex high speed TripleTOF™ 5600+ mass spectrometer (

For data processing, facility has licenses for Sciex ProteinPilot™, PeakView™, MarkerView™ software for proteomic studies.

Statistical analyses and bioinformatics are performed with R and IPA (Ingenuity Pathway Analysis).

Facility has access to MicroLC-MSTrap using Eksigent LC coupled with Sciex MSTrap 6500 mass spectrometer (


Prices are subject to change depending on the amount of samples and the study setup. We will give a quotation based on the our inquiry sheet information. Prices are divided to academic and non-academic categories.


To contact us on your mass spectrometry needs please fill in the our inquiry form and send it to Coordinator.

Head of the facility:

Hannu Uusitalo, M.D., Ph.D., FEBO
Professor and Chairman,
Chief Physician


Ulla Aapola
Tel: 045 322 6772
Room: ARVO F312

Street address: Arvo Ylpön katu 34, 33520 Tampere, Finland


Nättinen J, Jylhä A, Aapola U, Mäkinen P, Beuerman R, Pietilä J, Vaajanen A, Uusitalo H. Age-associated changes in human tear proteome. Clin Proteomics. 2019 Mar 30;16:11

Nättinen J, Jylhä A, Aapola U, Parkkari M, Mikhailova A, Beuerman R, Uusitalo H. Patient stratification in clinical glaucoma trials using the individual tear proteome. SciRep. 2018, 8:12038, doi:10.1038/s41598-018-30369-x.

Jylhä A, Nättinen J, Aapola U, Mikhailova A, Nykter M, Zhou L, Beuerman R, Uusitalo H. Comparison of iTRAQ and SWATH in a clinical study with multiple time points. ClinProteomics. 2018 Jul30;15:24. doi: 10.1186/s12014-018-9201-5. eCollection2018.

Vähätupa M, Nättinen J, Jylhä A, Aapola U, Kataja M, Kööbi P, Järvinen TAH, Uusitalo H, Uusitalo-Järvinen H. SWATH-MS Proteomic Analysis of Oxygen-Induced  RetinopathyReveals Novel Potential Therapeutic Targets. Invest Ophthalmol Vis Sci. 2018 Jul2;59(8):3294-3306. doi: 10.1167/iovs.18-23831.

Latonen L, Afyounian E, Jylhä A, Nättinen J, Aapola U, Annala M, Kivinummi K, Tammela T, Beuerman R, Uusitalo H, Nykter M, Visakorpi T. Integrative analysis of the proteome in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression. Nat.Commun. 2018

Nättinen J, Jylhä A, Aapola U, Enríquez-de-Salamanca A, Pinto-Fraga J, López-Miguel A, González-García MJ, Stern ME, Calonge M, Zhou L, Nykter M, Uusitalo H, Beuerman R. Topical fluorometholone treatment and desiccating stress change inflammatory protein expression in tears. Ocul. Surf. 2018;16(1):84-92

Mikhailova A, Jylhä A, Rieck J, Nättinen J, Ilmarinen T, Veréb Z, Aapola U, Beuerman R, Petrovski G, Uusitalo H, Skottman H. Comparative proteomics reveals human pluripotent stem cell-derived limbal epithelial stem cells are similar to native ocular surface epithelial cells. Sci Rep. 2015;5:14684

Hongisto H, Jylhä A, Nättinen J, Rieck J, Ilmarinen T,Veréb Z, Aapola U, Beuerman R, Petrovski G, Uusitalo H, Skottman H. Comparative proteomic analysis of  human embryonic stem cell-derived  and primary human retinal pigment  epithelium. Sci Rep. 2017;7:6016

Tong L, Zhou XY, Jylhä A, Aapola U, Liu DN, Koh SK, Tian D, Quah J, Uusitalo H, Beuerman RW, Zhou L. Quantitation of 47 Human Tear Proteins using High Resolution Multiple Reaction Monitoring (HR-MRM) Based-Mass Spectrometry. J. Prot 2015;115:36-48.

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