Proteomics Core Facility
Introduction
The Proteomics Core Facility is a research facility located at the Department of Biochemistry and Molecular Biology, at the University of Debrecen, Faculty of Medicine. The laboratory is dedicated to carry out targeted proteomics studies and to examine post-translational modifications of proteins enabling research principally in the Faculties of Science and Medicine of the University of Debrecen and undertakes research, collaborations and analytical services for other Universities and biotech companies in the proteomics field. The laboratory was established in part by the KMA 0149/3.0 grant from the Research Fund Management and Research Exploitation and the Department of Biochemistry and Molecular Biology (University of Debrecen) in 2005. In 2018 a considerable facility development happened thanks to the GINOP-2.3.3-15-2016-00020 grant.
Our mission is to undertake research and to provide access to state-of the art mass spectrometry technology and 2 dimensional electrophoresis techniques.
Our laboratoy was recognized as Top50 Research Infrastructure and awarded the title Excellent Research Infrastructure in Hungary.
Members
Members
Prof. Tőzsér, József - Core Facility Supervisor
Prof. Csősz, Éva - Core Facility Manager
Dr. Kalló, Gergő - research fellow
Prof. Márton, Ildikó - visiting professor
Kökényesiné Csáki, Julianna - lab technician
Kumar, Ajneesh - PhD student
Nokhoijav, Erdenetsetseg - PhD student
Guba, Adnrea - PhD student
Bertalan, Petra - PhD student
Szűcs, Nikolett - PhD student
Vadadokhau, Uladzislau - PhD student
Moagi, Mabuse - PhD student
Students in the Lab
Bui, Dan
Ayman, Jaxi
Szász, Dóra
Former Members
Dr. Boross, Peter - Core Facility Manager 2007-2008
Dr. Sperka, Tamas - Core Facility Manager 2005-2007
Bereczki, Kamilla - assistant
Kulcsár, Andrea - assistant
Emri, Zsófia - diploma student
Tóth, Emese - diploma student
Hegedűs, Zsuzsa - diploma student
Kicska, Lívia - diploma student
Labiscsák, Péter - Ph.D.student
Sipos, Beáta - diploma student
Bácsik, Viktória - diploma student
Joh, Sungmin - diploma student
Halász, Flóra - diploma student
Arany, József - diploma student
Molnár, Gábor - diploma student
Bokros, Csaba - diploma student
Pató, Zsuzsanna - Ph.D. student
Márkus, Bernadett - Ph.D. student
Deák, Eszter - Ph.D. student
Joóné Dr. Matúz, Krisztina - research fellow
Szabó, Emese - Ph.D. student
Kovács, Fruzsina - diploma student
Sinka, Laszlo - diploma student
Székely, Tímea - lab technician
Kovács, Renáta - technical assistant
Hartman, Zsolt - project assistant
Darai Zoltánné, Julika - lab technician
Böszörményi, Máté - diploma student
Vominh, Doan - diploma student
Tarsoly, Zsófia - diploma student
Varga, Anita Katalin - diploma student
Bába, Orsolya - diploma student
Bertók, Nikolett - diploma student
Prof. Prókai, László - visiting professor
Kenza Nigrou
Analytical services
The PCF provides analytical services in proteomics based on its equipment and expertise.
This includes analysis and method development for peptides and proteins:
- protein identification
- protein quantification by SRM
- label-free protein quantification
- protein quantification using chemical labeling (ex. iTRAQ)
- data evaluation
- protein/peptide cleanup using C18-containing tips
- protein cleanup prior two dimensional electrophoresis
- two dimensional electrophoresis in 7 and 25 cm formats
- gel documentation
- gel image analysis
- densitometry
- DIGE
- in gel or in solution digestion
Analyses are provided for research groups at University of Debrecen and affiliated institutions on an overall cost-recovery basis. Analytical services are also provided to non-UD institutions, commercial and international clients. Costs are discounted for groups from UD (and its affiliated institutes). Commercial fees are competitive and compare favourably with costs for similar services from other laboratories.
When data aquired from analytical services are published in the Acknolwdgement part the following sentence should be included:
"Mass spectrometric analysis for this work was carried out at the Proteomics Core Facility, Department of Biochemistry and Molecular Biology, University of Debrecen ."
In most cases the protocols for sample preparation and analysis are established via discussions with the staff of the PCF.
After the completion of the analyses the results are sent in electronic format for the Costumer and a report is generated and sent for signature. By signing the report the Costumer acknowledges the receipt of results.
Research collaborations, where the PCF makes intellectual contributions, usually involve some sharing of analysis costs. Research collaborations are not part of the Analytical Services and are described separately in the Research collaborations part of this site.
Costs - Price list
Costs are discounted for groups from University of Debrecen, Faculty of Medicine (and its affiliated institutes). Commercial fees are competitive and compare favourably with costs for similar services from other laboratories. The PCF provides some discounts for the spin-off companies of the UD and companies enrolled in the Bioincubator Project, helping their research and development actions.
Sample Submission
Samples may be delivered to the laboratory (University of Debrecen, Proteomics Core Facility, Theoretical Building 204., Nagyerdei krt. 98., 4032 Debrecen) or sent by post/courier.
Samples should be submitted with a signed Sample Submission Form. Only the samples for which the Sample Submission Form was completed will be accepted for analysis!
The following types of samples are regularly analysed in the PCF:
Proteins and peptides for mass spectrometry
Proteins and biological samples for 2D electrophoresis
In some cases it will be necessary for sampling and analysis protocols to be established in discussion with the PCF prior to analysis or sample submission. If in doubt contact us .
Download sample submission form documents:
Research collaboration
Collaborative projects begin with an informal discussion of the scope and aims of the work. Groups interested in collaboration should contact the PCF to arrange such a discussion.
Groups who do not require a large intellectual input from the PCF usually obtain their measurements via the analytical services.
Equipment
Mass spectrometers
- 4000 QTRAP (ABSciex) hybrid triple quadrupole/linear ion trap mass spectrometer equipped with Turbo V and NanoSpray electronspray ion sources, suitable for protein identification, post-translational modification detection and protein quantitation
- Orbitrap Fusion (Thermo Scientific) tribrid mass spectrometer equipped with ESI and nano ESI ion sources, ETD, HCD and CID collision techniques, suitable for protein identification, post-tranlstional modification detection, label-based and label-free quantification techniques, data-dependent and data-independent acquisition (DDA and DIA) methods.
HPLC
- Proxeon Easy nLC II (Bruker) nano LC for sample fractionation
- Thermo Easy nLC 1200 (Thermo) nano LC for sample fractionation
Equipments for electrophoresis
- BioRad IEF cell suitable for 7 cm, 11 cm, 17 cm and 24 cm strip analysis
- BioRad Mini-PROTEAN Tetra Cell
- BioRad PROTEAN II xi XL Cells
- BioRad PROTEAN Plus Multi-Casting Chamber
- BioRad PROTEAN Plus Dodeca Cell
- BioRad PharosFX Plus System for gel documentation
Utilized softwares
- ProteinPilot 4.5 (ABSciex) for protein identification and quantifiction
- MaxQuant (Max Plack Institute) for protein identification and quantification
- Delta2D (Decodon) for accurate 2DE gel image analysis
- QuantityOne (BioRad) for 1D gel image analysis
- Skyline (MacCoss Lab) for SRM transition design, optimization, data analysis and data publication (Panorama)
- BioPharma Finder 3.0 (Thermo Scientific)
- Xcalibur 4.1 (Thermo Scientific)
- Analyst 1.6 (ABSciex)
Ultracentrifuge
- Kontron ultracentrifuge
- Sorvall WX Ultra (Thermo Scientific) ultracentrifuge
- List of available rotors:
Repository
2 dimensional electrophoresis gel image repository
Proteomic analysis of protein phosphatase Z1 from Candida albicans
Control gel images (jpg)
Pro-Q Diamond stained gels (display by clicking on the gel identifier)
RuBPS stained gels (display by clicking on the gel identifier)
CaPpz1 KO gel images (jpg)
Pro-Q Diamond stained gels (display by clicking on the gel identifier)
RuBPS stained gels (display by clicking on the gel identifier)
Analysis results (download by clicking on the file name): Quantity table.xls
Conditions of use
University of Debrecen BMBI Proteomics Core Facility Conditions of Use
After sample analysis the BMBI Proteomics Core Facility sends to the Costumer a report and a bill containing the costs of the analyses. The report will be sent in electronic and printed formats as well. The printed format needs to be signed by the Costumer and should be sent back to the BMBI Proteomics Core Facility for record keeping purposes. You should note that the payment for the analyses is due even if the results generated are not the expected ones, but control runs prove that the equipment worked well and the analysis was done properly!
An appropriate acknowledgement of the involvement of the BMBI Proteomics Core Facility shall appear in any publication involving work in the BMBI Proteomics Core Facility. The following wording is suggested:
"Mass spectrometry analysis was carried out at the BMBI Proteomics Core Facility, Department of Biochemistry and Molecular Biology, University of Debrecen. "
Note also that often other grants/support would also need to be acknowledged.
If the BMBI Proteomics Core Facility is involved in assay development and/or validation work, co-authorship is required with the appropriate member(s) of the lab.
A copy (or full citation details, link) of any publication involving work in the BMBI Proteomics Core Facility should be sent to the facility manager as soon as possible after publication.
Submission of an analysis request form provides your agreement to the above conditions.
