Proteoomika tuumiklabor

Tartu Ülikooli proteoomika tuumiklabor (TÜ PTL) on mass-spektromeetrial (MS) põhinevaid proteoomika analüüse pakkuv teenuslabor. MS-proteoomika eesmärgiks on kirjeldada, nii kvalitatiivselt kui kvantitatiivselt, erinevate bioloogiliste proovide (koed, rakud, kehavedelikud jms) valgulist ja peptiidset koostist. Pakume teenuseid TÜ uurimisrühmadele ja teistele teadusasutustele nii Eestist kui välismaalt, samuti erasektorile.

Teenused:

Valkude tuvastamine ja sekveneerimine.
Valkude märgisevaba (’label-free’) ja märgisega (nt. SILAC) kvantiteerimine.
Valkude post-translatsiooniliste modifikatsioonide tuvastamine.

Võimalike küsimuste puhul soovitame võtta ühendust tuumiklabori juhi Ivar Ilvesega (ivar.ilves@ut.ee). Samuti palume meiega alati ühendust võtta enne proovide ettevalmistamist ja kohaletoomist, et panna koos paika sobiv katseplaan ja analüüsimeetod.

Kehtiv teenuste hinnakiri.

Proovide üleandmine ja transport.

Tuumiklabori tööde jooksev järjekord.

APARATUUR

TÜ PTLis on kasutusel järgmised instrumendid.

Elektroforees

Agilent 3100 OFFGel
Invitrogen XCell SureLock MiniCell SDS-PAGE
Expedeon GELFREE 8100

Vedelik-kromatograafia

Agilent 1200 Series nano-LC
Dionex Ultimate3000 RSLC nano-LC
Thermo Fisher Scientific Easy-nLC 1000

Mass-spektromeetria

Thermo Fisher Scientific Q Exactive Plus
Thermo Fisher Scientific Q Exactive HF

Ivar Ilves, PhD (molekulaarne viroloogia), tuumiklabori juhataja e-post: ivar.ilves@ut.ee

Merilin Saarma, MSc (bioloogia), spetsialist, e-post: merilin.saarma@ut.ee

VALIK PROTEOOMIKA TUUMIKLABORIGA SEOTUD PUBLIKATSIOONE

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.