Talking protein tags, novel ideas and tech innovation

5 November 2016
As one of our Expert Scientists, Sven Eyckerman knows all about the ‘tech’ in ‘biotechnology’.
Together with his VIB-Ghent University research team, he has been working on several innovative biotechnologies. A recent example is the generic Virotrap platform, as seen in VIBnews June. Shortly after, Sven and his team came up with yet another pioneering technique. They developed a set of universal protein tags that go by the acronym of ‘PQS’ and enable protein quantification via targeted proteomic techniques. Sven talks you through the how and why of this new tool and tech innovation in general.

Gaining an accurate view of a protein’s cellular concentration remains challenging: antibody-based approaches and alternative quantification strategies both have their own limits. In close-knit collaboration with two other VIB-UGent teams, Sven and his team members zoomed in on one specific, proteomic method: Selected Reaction Monitoring (SRM). Resulting in a brand-new research technique, their multi-disciplinary work was published in the online, open-access journal Scientific Reports.

What was the main trigger for developing this new research technique?
Sven: “SRM is a method that quantifies the ‘best mass spectrometry’ in a protein to monitor the expression level of that protein, its abundance so to speak. But there’s a catch: multiple of these ‘best’ peptides need to be selected for each studied protein, making assay development difficult. That’s why we envisioned a universal SRM assay based on protein tags.”

How did you turn this idea into a workable tool?
Sven: “We teamed up with the bioinformatics research group of Lennart Martens and the proteomics lab of Kris Gevaert. Together, we looked for peptides with excellent properties for SRM-based detection and quantification, properties that were absent from all the available proteomes of model organisms. These peptides can now be used as protein tags. That way, it’s no longer necessary to set up an SRM assay for each protein of interest, saving researchers a lot of time and effort.”

Does this open up new perspectives in your field of study?
Sven: “Using the CRISPR/Cas9 system, we also managed to effectively tag endogenous proteins. This adds a powerful new aspect to genome editing, crucial to new research. In addition, it is possible to address specific important biological issues that impact people’s lives.”

Where does your fascination with new technologies come from?
Sven: “When I was twelve, I remember getting a science book. The cover featured a picture of what looked like the Apollo lunar module that was used to land on the moon. It took me a few years to figure out what was really in the picture: an electron microscope image of a bacteriophage, a minuscule device that ‘lands’ onto bacteria to inject them
with a lethal substance. I think this finding prompted my interest to study biotechnology, while the people I met during my career further encouraged and inspired me.”

What usually kick-starts novel ideas?
Sven: “New ideas often come from a certain frustration about what is – or rather isn’t – possible using today’s research methods. To give just one example, it used to be impossible to investigate protein complexes without destroying the cell. That triggered us to come up with a new research technique: the Virotrap concept was born.

New ideas also pop up when I lie awake at night. Or when I perform repetitive tasks in the lab and let my mind wander. Coming to think of it, that might not always be beneficial for the experiment I’m carrying out... Seminars and conferences can get your creativity flowing as well, especially if they address topics outside your own research domain. Many technological developments are the result of a crosspollination occurring between two fields
of study.”


Techwatch: calling all innovation aficionados
Sven: “Technology is evolving almost ludicrously fast. Staying up-to-date has become quite a challenge, while early access to new technology can profoundly impact your research. That’s why VIB’s TechWatch is such a unique and powerful asset. Mark Veugelers and Halina Novak, responsible for TechWatch at VIB HQ, know exactly what’s possible technologically. Why not contact them directly about your research question or need, instead of browsing through the TechWatch technologies list on the website? And if certain technology turns out to be unavailable, I’m confident that VIB’s tech freaks will be happy to take the challenge!”

Vandemoortele G., Staes A., et al., Scientific Reports 2016

Sven Eyckerman (VIB-UGent)