This article can be enjoyed in an engaging digital feature format, as part of our Mass Spectrometry 2025 Special Edition, which also includes interviews with Boone Prentice and Susan Richardson.
How would you describe the current landscape of mass spectrometry in 2025?
It's especially wide open – and has been for a number of years now. Each year, I believe I understand the scope of this type of measurement, yet the field never fails to surprise me.
Years ago, we saw the emergence of powerful computers that enabled molecular and macromolecular structural computations. Then electrospray ionization came along, suddenly allowing us to make new types of large biological ions. These advances were accompanied by a revolution in genomics technologies – sequencing the first human genome – which led into proteomics, and metabolomics, lipidomics, glycomics, and so on. All of this has pushed us, broadly, towards diagnostics and the identification of new, targetable molecules for treating disease, or simply gaining an understanding of what happens when the genome makes a mistake. Around the time all this happened – five years or so into my career – it was hard to fathom a brighter future for the field of mass spectrometry.
Nowadays, we have advanced ionization sources that enable us to generate ions in so many different ways. If you can imagine it, chances are there's a way to ionize it. There are still some molecular classes we’re stumbling around with, but we have so many more options – and so many gentler ones. This allows us to preserve structure and begin using mass spectrometry in different ways, including in structural biology.
It’s also worth mentioning all these new “sniffing devices,” similar to what you might have seen used in an episode of Star Trek. A recent example is Graham Cooks’ DESI source, which enables direct probing of an environment with atmospheric pressure ionization. There are some – my former postdoc Sarah Trimpin, for one – who don’t believe you even need voltage to make ions anymore. Steve Valentine (one of my first graduate students – has a droplet-generating vibrating tip that can create ions across a continuum of potentials used in positive and negative ion electrospay, taking advantage of differences in ionization that we never would have imagined would generate ions years ago.
It’s fair to say that the ion source revolution is here – that’s something we now have at our disposal.
Looking back at the past year – ASMS 2025 in particular – what stood out to you, thematically or technically?
The big theme this year, in my opinion, was the megadalton to gigadalton regime – and this has now been extended into the teradaltons as noted in the fascinating work shown from Evan Williams’ group. I have to stop and think about what this range truly means; a megadalton is a million (where large protein complexes and viruses reside), a gigadalton is a billion (where extracellular vesicles are found), and a teradalton must be somewhere beyond that. When you stop and really think about it, it’s almost inconceivable.
In the MDa to GDa range we learned about a new generation of mass spectrometers that will become available (from Waters based on Martin Jarrold’s work) and a compact prototype from a new venture started by John Hoyes. In full disclosure, I am involved in helping Martin commercialize his charge detection mass spectrometry (CD:MS) technology with Waters Corporation (the instrument launch is scheduled for October). With it, you’ll be able to measure the masses of complexes, nanoparticles, aggregates – even cellular components that you’d never imagined were measurable – all with high fidelity. At ASMS, Evan Williams’ group even presented a measurement in the teradalton regime.
Back in 2009, I was invited to give a special lecture exploring the mass scale of the universe. I looked all the way up, from the total mass of the universe – including dark energy – down to the lowest-energy mass imaginable. And in the middle, there was this region which John Fenn was revolutionizing with electrospray ionization, going from a thousand, to perhaps even a million molecular weight. At the time, there were claims you could achieve higher, but no one could imagine ten million to a hundred million, or ten million to a billion – or even a trillion. It just blows your mind. And we’re just at the beginning; we know nothing about what’s up there at the level of fidelity and limits of detection that mass spectrometry can bring. So the fact that there are peaks – that these peaks even exist – is rather amazing.
The instrumental advances enabling these high mass ranges have been building over the past decade; and really started accelerating maybe five years ago. Now, I think you’ve got a lot of people interested in seeing what’s out there, asking questions such as: What are the assemblies of complex protein structures that are responsible for a certain physiological state in a cell? For the first time, that’s going to be measurable.
What would you say are the most pressing challenges currently facing the field?
I think one of the big challenges will be stabilizing large molecules of interest, as well as destabilizing them in such a way that removes all of the solvent, while producing a single peak in your mass analyzer. If you have big, broad distributions of water surrounding your analyte – and your particle looks more like a water droplet than the molecule you're interested in – you’ll never resolve species with high resolution. This is one of the major challenges right now.
The techniques themselves are very capable of going to high resolution – into the hundreds of thousands, even. But seeing that resolution will be hard, as we learn how to desolvate and desalt molecules that we haven’t previously dealt with before. And the tremendous heterogeneity that exists with high mass will be challenging. So the source – and cleanup – still needs a lot of work; and, it is likely that new models will be needed to understand very complex systems.
The second stage will be to learn about the molecules through these powerful techniques of dissociation we have at our disposal. The first approaches that come to mind are laser-based – combining energy with light – or to have molecules hit a surface, such as Vicki Wysocki’s work with SID for smaller molecules. I expect that breaking these big molecules apart by MS/MS, MS/MS/MS and higher order strategies will be tremendously important. I think Vicki referred to it years ago as “complex down” rather than “top down:” where you start with a large protein complex and then break it apart into its individual proteins, before breaking those into peptide ions to learn the sequences. There is then, of course, the challenge of building databases, models, and fragmentation rules for all of this.
We’re looking at molecules now that have post-translational modifications, and we don’t yet fully know how to deal with that. Often, these are stabilized by other parts of the cell – lipids may stabilize some regions and hold things together. Due to our limited understanding of this area, breaking each class of new complexes apart in an information rich way will be a milestone when it happens – key benchmarks for the field to build upon.
My group, in collaboration with Martin’s, submitted a paper recently using an ion mobility instrument on the front of a CD:MS system. That gives you a powerful new dimension of separation at the millisecond scale. Furthermore, Martin and his student Laura Young recently published an LC instrument on the front of one of their analyzers. Moving forward, we’ll see more multiple-dimensional setups emerging with CD:MS, and implementing all of this will be challenging.
Everything requires signals that are just barely in the regime of measurable right now. To give you some perspective: 30 years ago when we were starting, we literally had one ion every few seconds; it would take hours to get enough signal to see a peak. Mobility instruments now can measure analytes we couldn’t even dream of back then, but the sensitivity has had to come up many orders of magnitude to make that possible.
This will also be an area of importance for CD:MS. There will need to be new ways to make those measurements, just as there were for mobility cells. Nowadays, there are many ways to perform ion mobility, and I predict you’ll see many ways to do charge detection in the future as well.
We’re just at the beginning, and these are just the challenges I see. More interesting will be the ones we don’t see – rather, those we stumble into.
What sort of external influences – economic, regulatory, or otherwise – do you think are having the biggest impact on the field right now?
This field was a small one for at least 60 or 70 years, and one of the big drivers of its growth wasn’t proteomics or genomics – rather economics. Having industries interested in building and selling instruments really supported the field, providing another source of funding beyond solely federal grants. This has enabled the field’s migration away from physics-based problems and toward more applied problems – in other words, toward the more affluent area of medicine and drugs.
It took antibodies around 25 years to hit the market from when they were first proposed, and I feel we’re at a similar stage now with gene therapies. There are now more than 2,000 gene therapies at some stage of clinical development across various companies around the world. COVID therapeutics were a form of this and in some ways, the mRNA-based approaches worked, which is very exciting. But overall, we’re still at a very early stage. So having medicine as a driver – the potential to influence people’s wellness and cure rare diseases – is really powerful. You have these horrible one-off diseases in children, for example, that you can now imagine having a cure for.
All of these things are major drivers that help fund the development of mass spectrometry. With this in mind, having economics in our favor is a big advantage.
Looking towards the future, what do you think needs to happen (or change) to enable more meaningful progress in mass spectrometry?
I believe that one of our limitations is going to be in training the next generation of scientists. It’s a feeling I think many of us share.
Analytical chemistry is one of the smaller disciplines, though it is growing – in large part due to mass spectrometry. Having students is key, and a concern is that it's recently become difficult, primarily due to politics. We cannot overstate the impact of our foreign students on our success – the role they’ve played after coming to the United States; founding companies, working in industry, becoming professors. How are we possibly going to replace that impact?
The current political environment is such that, if I were a student studying abroad who dreamed of becoming a scientist in a country where I otherwise couldn’t be, I’d be hesitant. I still hope young graduates are looking at the U.S. as an option, because I think – without dismissing other countries – the U.S. PhD process is one of our great exports. We've imported and exported talent around the world in ways that have been profoundly impactful for science. Therefore, my concern is that we might enter a world where we lack the intellectual contributions and diversity of thought that we’ve benefited from.
Science is a meritocracy; we don’t put boundaries on ideas. Ideas don’t have political boundaries, and the notion that we would limit who can participate is upsetting. Of course, if you impact the overhead rate of universities, you damage the whole scientific endeavor. It costs a lot of money to run a university, but that really is more of a political problem too.
I think the biggest obstacle is remembering that we should be training more people around the world to understand the planet – we are a part of it, after all. Our removal of ourselves as human beings from the natural world is obviously a crazy idea. We have to participate in the world like all other organisms. But if I step back and ask what might set us back? Wars, political issues, these sorts of things come to mind.
What’s your overall outlook on the future of the field right now?
I think the field is moving in the right direction. I’m so bullish about the future – there’s rarely a day that I don’t see something that I find fascinating. The world has realized that, as an analytical technique, what could be more powerful than making a measurement of mass? It's incredibly sensitive and flexible.
These are amazing capabilities. There are still some things we can’t do yet, but if you really want to understand things at the molecular level – that’s only going to get better and better.
David E. Clemmer is the Robert & Marjorie Mann Chair of Chemistry at Indiana University Bloomington and a Distinguished Professor in the Department of Chemistry
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