Proteomics Facility Instruments and Software

Mass Spectrometry

Orbitrap Eclipse with FAIMS Pro Interface (Thermo Fisher)

The facility is equipped with the latest Tribrid mass spectrometer – Orbitrap Eclipse – which combines the best of quadrupole, linear ion trap and orbitrap mass analysers. The system offers enhanced ion transmission, extended m/z range for analysis of protein complexes in their native state and Real-Time Search which is used to identify MS2 peptides on the fly and trigger SPS MS3 data acquisition. This results in more effective cycle time usage while increasing the accuracy of quantitation. The Orbitrap Eclipse has also the option to be coupled to FAIMS Pro interface to increase sensitivity and orthogonal selectivity resulting in extended proteome coverage.

Liquid Chromatography

Thermo Ultimate 3000 RSLC System (Thermo Fisher)

Interfaced with the Orbitrap Eclipse for online peptide separation.

Thermo Ultimate 3000 HPLC System (Thermo Fisher)

The analytical HPLC is equipped with variable wavelength UV/VIS detector and automated fraction collection with the option of non-contiguous fraction concatenation. This system is used mostly to fractionate complex samples after TMT labelling to achieve maximum proteome coverage. It can collect fractions on 24 and 96 well plates or individual vials in the refrigerated autosampler. Number of final concatenated fractions is fully programable and depends on the complexity and goal of the project. The system operates in basic reverse phase for orthogonal peptide separation.

AKTA Pure (Cytiva)

The preparative HPLC is a flexible chromatography system for fast purification of proteins, peptides and nucleic acids. The system is available to book by all unit members upon request.

Automated sample preparation

Kingfisher Flex (Thermo Scientific)

The Kingfisher Flex is a highly versatile automated sample preparation/purification robot that uses magnetic-particle based protocols that can range from DNA/RNA, protein or cell purification. In the proteomics facility this robot is extensively used with “Single-pot, solid phase-enhanced samples preparation (SP3)” for high throughput sample digestion and sequential phosphopeptide enrichment protocols.