Proteomics Core

Mass spectrometry for proteome discovery and structural analysis.

In the Proteomics Core we use a wide range of techniques to address important biological questions.

We are equipped with four state-of-the-art mass spectrometers, which are employed to accurately identify, quantify, provide structural information and demonstrate interactions of proteins even in the most complex biological samples.

Our newest addition is a ZenoTOF 7600 mass spectrometer from Sciex. This fast and sensitive instrument enables high-throughput proteome analysis, even with low sample amounts. Additionally, the ZenoTOF includes a new fragmentation method that can improve the analysis of post-translational modifications.

We provide in-person training to the researchers on proteomic applications (experimental design, sample preparation and data analysis) and we offer an annual proteomics course on applications, experimental approaches and data interpretation.

Applications

Our Proteomics Core specialises in bottom-up proteomics. We offer a wide range of applications including:

  • In-depth Protein Identification with Data Dependent and Data Independent Acquisition
  • Post-Translational Modification analysis
  • Label-based (SILAC, TMT iTRAQ) and label-free quantitation analysis
  • High-throughput analysis with SWATH DIA
  • Targeted analysis

Along with the Rappsilber Lab that pioneered and optimised it, we offer Cross-Linking Mass Spectrometry (CLMS), and with the aid of our in-house search (https://www.rappsilberlab.org/software/xisearch/) and visualisation (https://xiview.org/index.php) software platforms, we are able to accurately identify and visualise cross-links that enable us to study protein-protein/RNA/DNA interactions and obtain structural information on proteins or protein complexes.

 

Equipment

Equipment available to Proteomics Core users:

ZenoTOF machine
  • Q Exactive™ Orbitrap Mass Spectrometer (Thermo Scientific)
  • Orbitrap Fusion™ Lumos™ Tribrid™ Mass Spectrometer (Thermo Scientific)
  • Orbitrap Exploris™ 480 Mass Spectrometer (Thermo Scientific)
  • Triple TOF® 6600+ System (Sciex) 
  • ZenoTOF 7600 (Sciex)

Each one of the orbitrap mass spectrometers is coupled online with a Dionex Ultimate 3000 nano-LC system. They are also equipped with an EASY-Spray™ ion source, allowing our columns to operate at a highly controlled temperature.

The Orbitrap Fusion™ Lumos™ Tribrid™ and Orbitrap Exploris™ 480 mass spectrometers are also equipped with the FAIMS technology, enabling differential ion mobility on existing workflows, expanding sample coverage.

The Triple TOF® 6600 system is coupled on line with a Waters Corporation nanoAcquity UPLC System, and the ZenoTOF is coupled with an Acquity M-Class UPLC.

Our proteomics Core is also equipped with an offline Dionex Ultimate 3000 UPLC System, dedicated to Reverse Phase High pH offline fractionation. 

Access to the DRP-HCB Proteomics Core

To access the Proteomics Core, you must first register a project with the DRP-HCB.

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