OMICS Proteomics

OMICS Proteomics

Mgr. Karel Harant

Mgr. Karel Harant — Laboratory head

About us

We offer complex proteome analysis and quantification on the latest generation of Mass spectrometry equipment–Thermo Orbitrap Fusion. We are able to quantify your sample on the whole proteome level using an untargeted approach or just a selected protein with a targeted analysis. The most common applications are: quantitative analysis of whole proteomes comparing, for example, treated and control samples, analysis of immunoprecipitated proteins and targeted quantification of selected peptides.

Our Services:

  • Preparation of samples for analysis (we are able to prepare a sample for analysis from your tissue or cell line)
  • Proteomic analysis of your samples – identification and quantification of proteins (aproximately 4500 quantified proteins from the human cell line in a single injection)
  • Data analysis and basic statistical evaluation
  • Consultation about experimental designs and how to obtain the maximum amount of informationfrom your experiment
     

CF SERVICES/SUCCESSFUL PROJECT

We are able to quantify your sample using different approaches – label free quantification, SILAC, isobaric tag quantification (iTRAQ), dimethyl labelling etc. We can also offer detection and quantification of various posttranslational modifications (PTMs), such as phosphorylation, acetylation or other PTMs. In addition to basic data analysis which is free for each sample, we can  perform more complex bioinformatic and statistical analysis or train your staff how to use proteomics software and how to interpret proteomic data.

POTENTIAL FOR COOPERATION:

We will be your partner in your research efforts. Each analysis is consulted individually beforehand to perfectly meet your demands. All our services are available for everybody from the academic and non academic areas. We work in pay per analysis mode and we don’t demand co-authorship on your publications. In case of stable and long-term cooperation You can obtain an individualized price quote.

News

Services

We are able to quantify your sample using different approaches – label free quantification, SILAC, isobaric tag quantification (iTRAQ), dimethyl labelling etc. We can also offer detection and quantification of various posttranslational modifications (PTMs), such as phosphorylation, acetylation or other PTMs. In addition to basic data analysis which is free for each sample, we can perform more complex bioinformatic and statistical analysis or train your staff how to use proteomics software and how to interpret proteomic data.

Our Services:

  • Preparation of samples for analysis (we are able to prepare a sample for analysis from your tissue or cell line)
  • Proteomic analysis of your samples – identification and quantification of proteins (aproximately 4500 quantified proteins from the human cell line in a single injection)
  • Data analysis and basic statistical evaluation
  • Consultation about experimental designs and how to obtain the maximum amount of informationfrom your experiment

Services

01

Princip necíleného proteomického experimentu

02

Notargeted proteomics

02

Targeted proteomics

03

targeted metabolomics

Equipment

Proteomic core facility

vacuum concentrator

vacuum concentrator

vacuum concentrator  without cooling , oil rotary vacuum pump

Software

Compound Discoverer 2.0

Compound Discoverer 2.0

http://planetorbitrap.com/compound-discoverer#.XFwbKlVKgUE

TraceFinder

TraceFinder

Software package for targeted SRM and MRM data acquisition, data processing and quantification

https://www.thermofisher.com/order/catalog/product/OPTON-30491

Software - Freeware

Publications

2019

Makki A., Rada P, Žárský V., Kereiche S., Kovacik L., Novotny M., Jores T., Rapaport D., Tachezy J. 2019 Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. PLoS Biology. 17(1):e3000098. doi: 10.1371/journal.pbio.3000098

  

Syslova, E., Landa, P., Stuchlikova, L.R., Matouskova, P., Skalova, L., Szotakova, B., Navratilova, M., Vanek, T. and Podlipna, R. (2019) Metabolism of the anthelmintic drug fenbendazole in Arabidopsis thaliana and its effect on transcriptome and proteome. Chemosphere, 218, 662-669.

Palyzová, A., Zahradník, J., Marešová, H., & Řezanka, T. (2019). Characterization of the catabolic pathway of diclofenac in Raoultella sp. KDF8. International Biodeterioration & Biodegradation, 137, 88–94. doi:10.1016/j.ibiod.2018.11.013

Jankovska, E., Svitek, M., Holada, K. and Petrak, J. (2019) Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage. Clin Proteomics, 16, 9.

Vit, O., Harant, K., Klener, P., Man, P. and Petrak, J. (2019) A three-pronged "Pitchfork" strategy enables an extensive description of the human membrane proteome and the identification of missing proteins. J Proteomics, 204, 103411.

Makukhin, N., Havelka, V., Polachova, E., Rampirova, P., Tarallo, V., Strisovsky, K. and Misek, J. (2019) Resolving oxidative damage to methionine by an unexpected membrane-associated stereoselective reductase discovered using chiral fluorescent probes. FEBS J.

Kohutova, J., Elsnicova, B., Holzerova, K., Neckar, J., Sebesta, O., Jezkova, J., Vecka, M., Vebr, P., Hornikova, D., Szeiffova Bacova, B. et al. (2018) Anti-arrhythmic Cardiac Phenotype Elicited by Chronic Intermittent Hypoxia Is Associated With Alterations in Connexin-43 Expression, Phosphorylation, and Distribution. Front Endocrinol (Lausanne), 9, 789.

2018

Van Nguyen P., Hlavacek O., Marsikova J., Vachova L., Palkova Z. (2018) Cyc8p and Tup1p transcription regulators antagonistically regulate Flo11p expression and complexity. PLoS genetics, https://doi.org/10.1371/journal.pgen.1007495

.Sykora, M., Pospisek, M., Novak, J., Mrvova, S., Krasny, L. and Vopalensky, V. (2018) Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin. PLoS Pathog, 14, e1007377.

Bilkova, B., Swiderska, Z., Zita, L., Laloe, D., Charles, M., Benes, V., Stopka, P. and Vinkler, M. (2018) Domestic Fowl Breed Variation in Egg White Protein Expression: Application of Proteomics and Transcriptomics. J Agric Food Chem, 66, 11854-11863.

Melenovsky, V., Cervenka, L., Viklicky, O., Franekova, J., Havlenova, T., Behounek, M., Chmel, M. and Petrak, J. (2018) Kidney Response to Heart Failure: Proteomic Analysis of Cardiorenal Syndrome. Kidney Blood Press Res, 43, 1437-1450.

Rossmeisl, M., Pavlisova, J., Janovska, P., Kuda, O., Bardova, K., Hansikova, J., Svobodova, M., Oseeva, M., Veleba, J., Kopecky, J., Jr. et al. (2018) Differential modulation of white adipose tissue endocannabinoid levels by n-3 fatty acids in obese mice and type 2 diabetic patients. Biochim Biophys Acta, 1863, 712-725.

Kuda, O., Brezinova, M., Silhavy, J., Landa, V., Zidek, V., Dodia, C., Kreuchwig, F., Vrbacky, M., Balas, L., Durand, T. et al. (2018) Nrf2-Mediated Antioxidant Defense and Peroxiredoxin 6 Are Linked to Biosynthesis of Palmitic Acid Ester of 9-Hydroxystearic Acid. Diabetes, 67, 1190-1199.

Rohde, F., Schusser, B., Hron, T., Farkasova, H., Plachy, J., Hartle, S., Hejnar, J., Elleder, D. and Kaspers, B. (2018) Characterization of Chicken Tumor Necrosis Factor-alpha, a Long Missed Cytokine in Birds. Front Immunol, 9, 605.

Mach, J., Bila, J., Zeniskova, K., Arbon, D., Malych, R., Glavanakovova, M., Nyvltova, E. and Sutak, R. (2018) Iron economy in Naegleria gruberi reflects its metabolic flexibility. Int J Parasitol.

Kuntova, B., Stopkova, R. and Stopka, P. (2018) Transcriptomic and Proteomic Profiling Revealed High Proportions of Odorant Binding and Antimicrobial Defense Proteins in Olfactory Tissues of the House Mouse. Front Genet, 9, 26.

2017

Cerna M, Kuntova B, Talacko P, Stopkova R, and Stopka P. 2017. Differential regulation of vaginal lipocalins (OBP, MUP) during the estrous cycle of the house mouse. Sci Rep 7:11674.

Erban, T., Harant, K., Chalupnikova, J., Kocourek, F. and Stara, J. (2017) Beyond the survival and death of the deltamethrin-threatened pollen beetle Meligethes aeneus: An in-depth proteomic study employing a transcriptome database. J Proteomics, 150, 281-289.

Stopkova R, Klempt P, Kuntova B, and Stopka P. 2017. On the tear proteome of the house mouse (Mus musculus musculus) in relation to chemical signalling. PeerJ 6:e3541.

Valis, K., Grobarova, V., Hernychova, L., Buganova, M., Kavan, D., Kalous, M., Cerny, J., Stodulkova, E., Kuzma, M., Flieger, M. et al. (2017) Reprogramming of leukemic cell metabolism through the naphthoquinonic compound Quambalarine B. Oncotarget, 8, 103137-103153.

Stafkova, J., Rada, P., Meloni, D., Zarsky, V., Smutna, T., Zimmann, N., Harant, K., Pompach, P., Hrdy, I. and Tachezy, J. (2017) Dynamic secretome of Trichomonas vaginalis: Case study of beta-amylases. Mol Cell Proteomics.

Vyklicka, L., Boukalova, S., Macikova, L., Chvojka, S. and Vlachova, V. (2017) The human transient receptor potential vanilloid 3 channel is sensitized via the ERK pathway. J Biol Chem.

Vosahlikova, M., Ujcikova, H., Chernyavskiy, O., Brejchova, J., Roubalova, L., Alda, M. and Svoboda, P. (2017) Effect of therapeutic concentration of lithium on live HEK293 cells; increase of Na+/K+-ATPase, change of overall protein composition and alteration of surface layer of plasma membrane. Biochim Biophys Acta, 1861, 1099-1112.

2016

Hartmannova, H., Piherova, L., Tauchmannova, K., Kidd, K., Acott, P.D., Crocker, J.F., Oussedik, Y., Mallet, M., Hodanova, K., Stranecky, V. et al. (2016) Acadian variant of Fanconi syndrome is caused by mitochondrial respiratory chain complex I deficiency due to a non-coding mutation in complex I assembly factor NDUFAF6. Hum Mol Genet, 25, 4062-4079.

Manakov, D., Ujcikova, H., Pravenec, M. and Novotny, J. (2016) Alterations in the cardiac proteome of the spontaneously hypertensive rat induced by transgenic expression of CD36. J Proteomics, 145, 177-186.

Stopka P, Kuntova B, Klempt P, Havrdova L, Cerna M, and Stopkova R. 2016. On the saliva proteome of the Eastern European house mouse (Mus musculus musculus) focusing on sexual signalling and immunity. Sci Rep 6:32481.

Vit, O., Man, P., Kadek, A., Hausner, J., Sklenar, J., Harant, K., Novak, P., Scigelova, M., Woffendin, G. and Petrak, J. (2016) Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments. J Proteomics, 149, 15-22.

Ujcikova, H., Vosahlikova, M., Roubalova, L. and Svoboda, P. (2016) Proteomic analysis of protein composition of rat forebrain cortex exposed to morphine for 10days; comparison with animals exposed to morphine and subsequently nurtured for 20days in the absence of this drug. J Proteomics, 145, 11-23.

Team

Mgr. Karel Harant

Mgr.
Karel Harant

Head of Proteomic Core Facilty

karel.harant@natur.cuni.cz
+420325873925
Mgr. Pavel Talacko

Mgr.
Pavel Talacko

Non-targeted proteomics, targeted proteomics

pavel.talacko@natur.cuni.cz
+420325873925
RNDr. Petr Žáček, Ph.D.

RNDr.
Petr Žáček, Ph.D.

GC / MS specialist, small molecule analysis

zacek@natur.cuni.cz
+420325873925
Mgr. Anna Březinová

Mgr.
Anna Březinová

LC/MS Specialist, small molecule analysis

anna.brezinova@natur.cuni.cz
+420325873925
Mgr. Veronika Ševců

Mgr.
Veronika Ševců

researcher, preparation of proteomic samples

veronika.sevcu@natur.cuni.cz
+420325873925