Proteomics Unit

The two main workflows are illustrated in the figure above.

In most cases, samples are analysed using data-independent acquisition (DIA), as this approach provides a high number of protein identifications combined with robust and reproducible quantification.

For specific applications, data-dependent acquisition (DDA) is also available. This is particularly relevant for experiments based on isobaric labelling strategies, such as tandem mass tags (TMT), which enable multiplexed analysis of multiple samples within a single experiment.

For projects requiring increased proteome coverage, we offer in-depth protein profiling workflows. These approaches are designed to maximise the number of identified proteins, including low-abundance species, by combining optimized sample preparation with extended chromatographic separation and/or fractionation strategies.

Such workflows typically involve additional sample processing steps and increased instrument time, and are therefore best suited for discovery-driven studies where comprehensive proteome coverage is a priority.

We offer workflows for analysing post‑translational modifications (PTMs), enabling insight into protein regulation beyond abundance changes through selective enrichment of modified peptides prior to LC‑MS.

Our main focus is phosphoproteomics for profiling signalling pathways, with additional PTM analyses available upon request. These workflows require specialised sample preparation and are best suited for studies of regulatory mechanisms and dynamic cellular responses.

We have two mass spectrometers and three different liquid chromatography systems. The standard configuration is Evosep - Exploris and Vanquish Neo - Eclipse. The Dionex 3000 can be flexibly coupled to either of the mass specs. Both of our mass specs are equipped with a High-Field Asymmetric-Waveform Ion Mobility Spectrometry (FAIMS) device. 

Orbitrap Eclipse                        Orbitrap Exploris 480

Evosep ONE                                Vanquish Neo                             Dionex Ultimate 3000

Early contact with PROBE is strongly recommended, particularly for new users or when working with novel sample types, as it enables optimisation of experimental design, sample preparation, and overall outcomes.

Samples should preferably be submitted as digested, desalted peptides ready for LC‑MS. If preparation is performed at PROBE, provide lysates with protein concentration information and include an aliquot of the lysis buffer. For standard workflows, ~30 µg protein per sample is typically sufficient. A lysis buffer of 4% SDS in 0.1 M Tris-HCl (pH 7.6) is suitable for many samples, with downstream processing using SP3 protocols. Guidance is available on request. Radioactive samples cannot be processed.

New users must contact probe@uib.no to discuss their project before starting a proteomics experiment. This helps ensure optimal experimental design and efficient use of our services.

All users must register in BookitLab before sample submission and data acquisition. Please ensure your research group is registered first by the PI to avoid delays. Detailed guidance is available in the BookitLab user guidelines.

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