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The Proteomics and Mass Spectrometry Core Facility

The Proteomics and Mass Spectrometry Core Facility provides proteomic services to researchers working at the Malopolska Centre of Biotechnology and external users from academia and the industry. Offered services include molecular weight determination of peptides and proteins, detection of posttranslational modifications as well as identification of proteins in complex proteome. We perform complete proteomic workflow covering sample preparation, protein digestion, mass spectrometry measurement and data analysis. Tandem mass spectrometry, as a robust, sensitive and precise technique, enables to identify and quantify thousands of different proteins in one experiment. 

 

EQUIPMENT:

The Proteomics and Mass Spectrometry Core Facility is equipped with two mass spectrometers, which are used depending on the sample requirements:

 

  • Q-Exactive coupled online to an Ultimate 3000 nanoLC-system (Thermo Scientific). It is a hybrid mass spectrometer, which  combines high-performance quadrupole precursor selection with high-resolution, accurate-mass Orbitrap™ detection. Principally used for protein identification and quantification in complex samples (e.g. cell lysates), as well as identification of post-translational modifications. HCD (high resolution) fragmentation enables application of MS2 quantification strategies (e.g. iTRAQ labelling).
  • micrOTOF-Q II (Bruker Daltonics) coupled online to an Ultimate 3000 nanoLC-system (Dionex). It is applied to protein identification in low-complex samples (e.g. from polyacrylamide gels). It is also used to measure molecular weight of intact proteins, peptides or nucleic acid fragments.

 

Software:

  • Mascot (Matrix Science)
  • Data Analysis (Bruker Daltonics)
  • Protein Scape (Bruker Daltonics)
  • Proteome Discoverer (Thermo Scientific)
  • MaxQuant (Max Planck Institute for Biochemistry, Martinsried, Germany)
  • Perseus (Max Planck Institute for Biochemistry, Martinsried, Germany)

AVAILABLE SERVICES:

  • Molecular weight determination of peptide or intact protein by ESI-MS - REQUEST FORM
  • Protein identification from polyacrylamide gel by nanoLC-MS/MS - REQUEST FORM
  • Identification and site-localization of selected post-translational modifications of purified protein proteins (acetylation, methylation, phosphorylation and others) by nanoLC-MS/MS - REQUEST FORM
  • Identification of proteins after co-immunoprecipitation by nanoLC-MS/MS - REQUEST FORM
  • Identification of proteins in complex proteomes by nanoLC-MS/MS - REQUEST FORM

 

Please fill in the request form and provide it with your samples.

SAMPLE PREPARATION METHODS:

  • In-solution/in-gel trypsin digestion
  • FASP
  • SP3 extraction
  • Desalting (Zip Tip, StageTips C18/SAX/SCX)
  • MED-FASP (digestion with trypsin and LysC) + SAX fractionation

Price list for internal and external users

PUBLICATION POLICY:

Apart from routine services we also apply individual solutions to meet various research needs. Collaborative projects that require non-routine sample preparation or data analysis justifies a co-authorship on a manuscript that contains data generated in our facility.

SCIENTIFIC COLLABORATION OFFER:

  • Relative quantification of proteins in complex mixtures (labelled and label-free)
  • Quantitative analysis of co-immunoprecipitation
  • Analysis of protein modification for enriched proteins on a global scale (e.g. phosphoproteomics)

GENERAL TIPS:

  • Avoid detergents, especially PEG, Triton, NP-40.
  • Keep sample on ice if non-denaturing buffer is used and use protease/phosphatase inhibitors.
  • Before analysis store gel bands at 4°C and other samples at -20°C.

Keratin is a common protein contaminate in mass spectrometry. Keratin originates from skin and hair and is present in dust. If keratins are present in high concentrations in samples, they cause decreased efficiency of protein identification. To improve the efficiency of protein identification:        

  • Use high-grade reagents and fresh buffers.
  • Use non-latex gloves and wear lab coats.
  • Close tubes, tip boxes after use.

CONTACT:

Please contact with Urszula Jankowska for consulting sample preparation and design of experiment before you start a project.

 

Urszula Jankowska, PhD
Head of Proteomics and Mass Spectrometry Core Facility
E-mail: urszula.jankowska@uj.edu.pl
Phone: +48 12 664 6096
Room: MCB 1/40

Natalia Radczuk, PhD
Adjunct
E-mail: natalia.radczuk@uj.edu.pl
Phone: +48 12 664 6096
Room: MCB 1/40

 

 

Address:

Malopolska Centre of Biotechnology
Proteomics and Mass Spectrometry Core Facility
Gronostajowa 7A
30-387 Krakow
Poland