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 DebrecenFaculty 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.

Our mission is to undertake research and to provide access to mass spectrometry technology and 2 dimensional electrophoresis techniques.

Members

Members

Prof. Tőzsér, József - Core Facility Supervisor

Dr. Csősz, Éva - Core Facility Manager

Bereczki, Kamilla - assistant

Kalló, Gergő - Ph.D. student

Jakob, Bernadette - Ph.D. Student

Deák, Eszter - Ph.D. Student

Pató, Zsuzsanna - Ph.D. Student

 

Students in the Lab

Székely, Tímea

Arany, József

Molnár, Gábor

 

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

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 molecular weight determination
protein quantification by SRM
protein quantification using chemical labeling (ex. iTRAQ)
data evaluation using ProteinPilot 4.5
protein/peptide cleanup using ZipTip
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 trypsin digestion
UV detector coupled nanoHPLC separations/analyses
multiplex assay implementation and measurement on BioPlex (BioRad) workstation
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 were carried out at the Proteomics Core Facility, University of Debrecen, Biochemistry and Molecular Biology Department."

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.

Pricelist Proteomics

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:
Biological samples for multiplex Luminex-based assays
Proteins and peptides for ESI and MS/MS
Proteins and peptides for MALDI-TOF
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 .

Users of the PCF Analytical Services agree to the following:

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/Luminex 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) 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.

Download sample submission form documents:

 

Research collaboration

Our major role is to facilitate fundamental and applied research where mass spectrometry is needed. Groups that do not have expertise in mass spectrometry may choose to collaborate with us. In these cases there is significant intellectual input from the PCF and the work is published jointly. These collaborations usually seek funding to cover the analysis costs within realistic limits that the funding schemes will allow. These are typically much less than the actual costs which are subsidised by University of the Debrecen. Longer term continuation of collaborations is usually contingent upon funding and publications being forthcoming.

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

  • Applied Biosystems Voyager-DE PRO MALDI-TOF for accurate molecular weight determination and peptide mass fingerprinting
 
  • Applied Biosystems 4000 QTRAP equipped with Turbo V and NanoSpray electronspray ion sources a high performance hybrid triple quadrupole/linear ion trap LC/MS/MS mass spectrometer suitable for protein identification, post-translational modification detection and protein quantitation

HPLC

  • Proxeon Easy nLC II (Bruker) nano LC for sample fractionation
  •  
  • Agilent 1100 nano LC for chromatographic separations

Luminex-based multiplex analysis

  • Bioplex system (BioRad)

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

Softwares

  • ProteinPilot 4.5 (ABSciex) for protein identification and quantifiction
  •  
  • Delta2D (Decodon) for accurate 2DE gel image analysis
  •  
  • PDQuest (BioRad) for 2DE gel image analysis
  •  
  • QuantityOne (BioRad) for 1D gel image analysis
  •  
  • MRMPilot (ABSciex) for SRM transition design
  •  
  • MultiQuant (ABSciex) for SRM data analyisis
  •  
  • Skyline (MacCoss Lab) for SRM transition design, optimization, data analysis and data publication (Panorama)

Ultracentrifuge

  • Kontron ultracentrifuge
  • Sorvall WX Ultra (Thermo Scientific) ultracentrifuge  
  • List of available rotors: 
 

Name

Max. RPM

1

Beckman JS-13.1

13000

2

Beckman JS-7.5

7 500

3

Kontron Type 50

50 000

4

Kontron TYP TFT 45.94

45 000

5

Kontron Type 35

35 000

6

Kontron SW 41 TI

41 000

7

Kontron SW 27

27 000

8

Kontron SW 55 TI

55 000

9

Kontron Type 50.4 TI

50 000

10

Kontron Type 19

19 000

11

Kontron TFT 50.38 Ti

50 000

 

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)

Ctl1_P, Ctl2_P, Ctl3_P

RuBPS stained gels (display by clicking on the gel identifier)

Ctl1_R, Ctl2_R, Ctl3_R

CaPpz1 KO gel images (jpg)

Pro-Q Diamond stained gels (display by clicking on the gel identifier)

Mut1_P, Mut2_P, Mut3_P,

RuBPS stained gels (display by clicking on the gel identifier)

Mut1_R, Mut2_R, Mut3_R,

Analysis results (download by clicking on the file name): Quantity table.xls