Proteomics core facility
The Proteomics Core Facility (PCF) of University of Tartu (UT) is a mass spectrometry (MS) based proteomics competence center. The goal of MS proteomics is to characterize both qualitatively and quantitatively the peptide/protein composition of cells, tissues, bodily fluids and biologics (e.g. therapeutic antibodies).
The facility is maintained on the basis of service analyses and concentrates the necessary instrumentation and qualified personnel for maintaining the apparatus. We offer our services to research groups within UT and for other scientific institutions (universities, national laboratories and others), also, for the biotechnology industry.
UT PCF offers following proteomics services:
• Protein identification and de novo sequencing.
• Protein label-free and label-based (e.g. SILAC, iTRAQ, TMT) relative and absolute quantification.
• Protein PTM identification, mapping and quantification:
o Phosphorylation, including enrichment of the specific modification,
o Methylation and acetylation, including enrichment of the specific modification,
o N- and O-glycosylation sites, ubiquitinylation sites and occupancy,
o Sulfation, nitration, deamidation, hydroxylation and other non-complex modifications,
o Characterization of glycans.
• Intact protein mass measurement and top-down identification (< 200 kDa).
• Endogenously (e.g. disulfide bridges) and chemically cross-linked peptide identification.
• Protein/peptide targeted (’parallel reaction monitoring’) quantitation.
• Protein biomarker discovery and verification services.
In addition to service analyses, UT PCF continually participates in scientific research and collaboration. The research of our scientists has been published in a number of different publications. Starting from 2019 UT PCF also participates in the pan-EU infrastructure project, EPIC-XS (https://epic-xs.eu/), which unifies leading proteomics groups over the EU to provide access and advance proteomics technologies.
Before submitting samples please contact the facility manager (e-mail: sergo.kasvandik@ut.ee) to discuss the details of your experimental design, so that the analysis can be optimally tailored to your needs.
The prices for different services can be found here.
For sample submission and transport to UT PCF, please read the relevant instructions and requirements.
The current UT PCF analysis queue can be monitored from here.
INSTRUMENTATION
The following instruments are available at UT PCF.
Electrophoresis
• Agilent 3100 OFFGel
• Invitrogen XCell SureLock MiniCell SDS-PAGE
• Expedeon GELFREE 8100
Liquid chromatography
• Agilent 1200 Series nano-LC
• Dionex Ultimate3000 RSLC nano-LC
• Thermo Fisher Scientific easy-nLC 1000
Mass spectrometers
• Thermo Fisher Scientific Q Exactive Plus
• Thermo Fisher Scientific Q Exactive HF
Sergo Kasvandik, PhD (medicine), facility manager, phone: +372 737 4842, e-mail: sergo.kasvandik@ut.ee
Merilin Saarma, MSc (biology), technician, e-mail: merilin.saarma@ut.ee
Kadi-Anne Nadel, MSc (materials science), technician, e-mail: kadi-anne.nadel@ut.ee
Publications
Pochopien, A. A.; Beckert, B.; Kasvandik, S.; Berninghausen, O.; Beckmann, R.; Tenson, T.; Wilson, D. N., Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Proceedings of the National Academy of Sciences 2021, 118, (14).
Crowe-McAuliffe, C.; Takada, H.; Murina, V.; Polte, C.; Kasvandik, S.; Tenson, T.; Ignatova, Z.; Atkinson, G. C.; Wilson, D. N.; Hauryliuk, V., Structural basis for bacterial ribosome-associated quality control by RqcH and RqcP. Molecular Cell 2021, 81, (1), 115-126. e7.
Kasvandik, S.; Saarma, M.; Kaart, T.; Rooda, I.; Velthut-Meikas, A.; Ehrenberg, A.; Gemzell, K.; Lalitkumar, P. G.; Salumets, A.; Peters, M., Uterine fluid proteins for minimally invasive assessment of endometrial receptivity. The Journal of Clinical Endocrinology & Metabolism 2020, 105, (1), 219-230.
Campbell, K.; Westholm, J.; Kasvandik, S.; Di Bartolomeo, F.; Mormino, M.; Nielsen, J., Building blocks are synthesized on demand during the yeast cell cycle. Proceedings of the National Academy of Sciences 2020, 117, (14), 7575-7583.
Mutso, M.; Morro, A. M.; Smedberg, C.; Kasvandik, S.; Aquilimeba, M.; Teppor, M.; Tarve, L.; Lulla, A.; Lulla, V.; Saul, S., Mutation of CD2AP and SH3KBP1 binding motif in alphavirus nsP3 hypervariable domain results in attenuated virus. Viruses 2018, 10, (5), 226.
Ahlstrand, T.; Torittu, A.; Elovaara, H.; Välimaa, H.; Pöllänen, M. T.; Kasvandik, S.; Högbom, M.; Ihalin, R., Interactions between the Aggregatibacter actinomycetemcomitans secretin HofQ and host cytokines indicate a link between natural competence and interleukin-8 uptake. Virulence 2018, 9, (1), 1205-1223.
Lahtvee, P.-J.; Sánchez, B. J.; Smialowska, A.; Kasvandik, S.; Elsemman, I. E.; Gatto, F.; Nielsen, J., Absolute quantification of protein and mRNA abundances demonstrate variability in gene-specific translation efficiency in yeast. Cell systems 2017, 4, (5), 495-504. e5.
Huter, P.; Arenz, S.; Bock, L. V.; Graf, M.; Frister, J. O.; Heuer, A.; Peil, L.; Starosta, A. L.; Wohlgemuth, I.; Peske, F., Structural basis for polyproline-mediated ribosome stalling and rescue by the translation elongation factor EF-P. Molecular cell 2017, 68, (3), 515-527. e6.
Resch, U.; Tsatsaronis, J. A.; Le Rhun, A.; Stübiger, G.; Rohde, M.; Kasvandik, S.; Holzmeister, S.; Tinnefeld, P.; Wai, S. N.; Charpentier, E., A two-component regulatory system impacts extracellular membrane-derived vesicle production in group A Streptococcus. MBio 2016, 7, (6).
Mumm, K.; Ainsaar, K.; Kasvandik, S.; Tenson, T.; Hõrak, R., Responses of Pseudomonas putida to zinc excess determined at the proteome level: Pathways dependent and independent of ColRS. Journal of proteome research 2016, 15, (12), 4349-4368.
Kasvandik, S.; Sillaste, G.; Velthut‐Meikas, A.; Mikelsaar, A. V.; Hallap, T.; Padrik, P.; Tenson, T.; Jaakma, Ü.; Kõks, S.; Salumets, A., Bovine sperm plasma membrane proteomics through biotinylation and subcellular enrichment. Proteomics 2015, 15, (11), 1906-1920.
Kasvandik, S.; Samuel, K. l.; Peters, M.; Eimre, M.; Peet, N. d.; Roost, A. M.; Padrik, L.; Paju, K.; Peil, L.; Salumets, A., Deep quantitative proteomics reveals extensive metabolic reprogramming and cancer-like changes of ectopic endometriotic stromal cells. Journal of proteome research 2015, 15, (2), 572-584.
Starosta, A. L.; Lassak, J.; Peil, L.; Atkinson, G. C.; Virumäe, K.; Tenson, T.; Remme, J.; Jung, K.; Wilson, D. N., Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site. Nucleic acids research 2014, 42, (16), 10711-10719.
Arike, L.; Peil, L., Spectral counting label-free proteomics. In Shotgun Proteomics, Springer: 2014; pp 213-222.
Peil, L.; Starosta, A. L.; Lassak, J.; Atkinson, G. C.; Virumäe, K.; Spitzer, M.; Tenson, T.; Jung, K.; Remme, J.; Wilson, D. N., Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P. Proceedings of the National Academy of Sciences 2013, 110, (38), 15265-15270.
Peil, L.; Starosta, A. L.; Virumäe, K.; Atkinson, G. C.; Tenson, T.; Remme, J.; Wilson, D. N., Lys34 of translation elongation factor EF-P is hydroxylated by YfcM. Nature chemical biology 2012, 8, (8), 695-697.
