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The Proteomics and Mass Spectrometry (MS) core facility of Department CIBIO will give researchers access to state-of-the-art instrumentation for characterization of proteins and complex proteomes. By using MS-based methods, which might have to be developed on a case-by-case basis, protein identification and quantification as well as analysis of posttranslational modifications can be performed. Characterization of small molecules will also be possible. 

The platform includes dedicated space and equipment for sample preparation, MS analysis and data analysis. 

Our main goal is to offer advanced technologies and high quality data to support researchers in a highly collaborative environment.

Main Services

Services offered by the Facility include:

  • Identification of proteins in complex samples, such as cells, tissues, organelles and vesicles and biofluids.
  • Differential quantification of proteins (e.g. health vs diseases) by using label based approaches (e.g. SILAC and TMT), label-free or targeted strategies.

  • Absolute quantification of proteins to monitor biological processes by using heavy labelled synthetic peptides
  • Post translational modifications (PTMs) of proteins, such as - but not only - methylation, acetylation or phosphorylation. 
  • Protein-protein and drug-protein interactomics as well as pathway characterization

Mass spectrometry

Ultraflex III (Bruker): A time-of-flight system equipped with a MALDI ion source mainly used for identification of protein (simple mixture only).

Fusion (Thermo Scientific): The highly performing tribrid system, equipped with ESI and nano-ESI ion sources. It is mainly used for characterization of proteins. It can be used for complex samples. Several options are available as fragmentation cells (collision-induced dissociation -CID, high-energy collisional dissociation –HCD and electron-transfer dissociation -ETD) and mass analysers (quadrupole, linear ion trap and Orbitrap®). 

Liquid chromatography

UltiMate 3000 RSLC System (Thermo Scientific Dionex): An analytical HPLC system used for intact proteins, primary and secondary metabolite separation. It can operate as a standalone system or interfaced directly with the ESI-MS/MS system. It is equipped with Diode Array and Multi-Wavelength Detector (DAD) and fractions collector.

Easy-nLC 1200 (Thermo Scientific): A binary ultra-high pressure UHPLC system used for peptide separation. It was designed for better performance and higher throughput and it is interfaced directly with the ESI-MS/MS system. Separation can be performed on commercial or in-house made nanocolumns.

UltiMate 3000 RSLCnano System (Thermo Scientific Dionex): A ternary ultra-high pressure LC system with nano or capillary flow options to maximize throughput capabilities and experiment multidimensional applications. The system is integrated with a UV/VIS detector for quantitative analysis and can operate as a standalone system or directly interfaced with the ESI-MS/MS system.