Chemists break barriers and open up super-resolution molecule mass analysis

Research team measures individual giant molecules with record-breaking precision

By modifying and boosting lab equipment, a team of chemists are able to measure individual molecules with unprecedented precision. This precision relates to being able to tell that one single sugar grain is missing from a full 1 kilogram bag of sugar. Their massive resolution upgrading will benefit the fabrication of vaccines and molecular vectors used in gene therapy. The team publish their results today in the journal Nature Methods.

Researcher Victor Yin in front of the modified mass spectrometer used to break the mass resolution record.
Researcher Victor Yin in front of the modified mass spectrometer used to break the mass resolution record.

A team of chemists led by Prof. Albert Heck puts a new spin on analysing and understanding molecules. By ingeniously improving current measuring equipment, the team were able to trap and observe individual molecules for a much longer period—up to 25 seconds. This extended observation time enabled them to see finer details of molecules, enhancing their understanding.

The precision upgrade is comparable to measuring a mass difference of one in a million. Heck compares it to a bag of sugar. “This precision relates to being able to tell that one sugar grain is missing from a full bag of 1 kilogram of sugar”, says Heck.

Evolène Deslignière
Researcher Evolène Deslignière, one of the chemists in Prof. Albert Heck's team and first author of the Nature Methods publication.

A thousand times longer

Traditionally, chemists use a technology called mass spectrometry to examine the composition of molecules. Although this offers analyses in substantial levels of detail, its downside is that is looks at millions of molecules at once. This makes it tricky to study large molecules, because the higher number of trapped molecules interfere with each other.

So, they developed a new method whereby just a single molecule is trapped in a so-called Orbitrap while heavily spinning. By measuring the spinning behaviour, they are able to analyse the mass and composition of the molecule.

Normally this method can only record signals for a short duration, typically around 25 milliseconds. In their study, the scientists modified the data acquisition method, allowing them to trap and monitor individual ions thousand times longer, for up to an impressive 25 seconds.

Spinning and swinging

To understand this advancement, imagine swinging on a swing for just a few seconds versus swinging for a prolonged period. The longer you swing, the more accurately an observer can measure your rhythm and deduce characteristics about you. Similarly, by trapping spinning ions for an extended duration, scientists can capture more detailed information about their spinning frequency and thus better characterize molecules.

Improving gene therapy

Being able to measure giant molecules in such detail could pave the way for advancements in various fields, says Heck. One example is the production of therapeutic molecules, such as viruses clinically used in gene therapy. These viruses are loaded with a human correctly functioning gene that replaces erroneous genes in the DNA of patients suffering from a genetic disorder.

Using the new method, gene therapy developers could make their production lines more efficient

Heck: “Up until now, developers of gene therapy viruses cannot really verify if a virus harbours the specific gene that it is supposed to deliver. It is estimated that by current methods only 1 to 2 percent of the produced gene therapy viruses are successfully loaded with the desired gene. This induces to that a substantial part of the therapeutic viruses introduced in a patient will have no effect.”

More accurate and efficient

If gene therapy developers can better measure the difference between ‘empty’ versus ‘filled’ viruses, they could make their production lines more efficient. Heck: “When you consider that some of the gene therapy treatments costs around 1 million euros per treatment, this efficiency improvement could have a significant beneficial impact.”

Collaboration and funding

In this study, Heck’s team closely cooperated with researchers from technology companies Spectroswiss and Thermo Fisher Scientific. The study was partly funded with Heck’s Spinoza Prize, awarded by the Dutch Research Council (NWO). The Spinoza prize is regarded as the highest academic award in the Netherlands.


Ultra-long Transients Enhance Sensitivity and Resolution in Orbitrap-based Single Ion Mass Spectrometry
Evolène Deslignière, Victor C. Yin, Eduard H.T.M. Ebberink, Amber D. Rolland, Arjan Barendregt, Tobias P. Wörner, Konstantin O. Nagornov, Anton N. Kozhinov, Kyle L. Fort, Yury O. Tsybin, Alexander A. Makarov, Albert J.R. Heck
Nature Methods, 5 March 2024. DOI: 10.1038/s41592-024-02207-8