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Rainer Cramer on IR MALDI and the University of Reading s New BioCentre

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At A Glance

Name: Rainer Cramer

Position: Director of BioCentre hub for post-genomic research, University of Reading, since Jan. 2005. Head of mass spectrometry and proteomics unit at BioCentre.

Background: Researcher, leader of mass spectrometry group, Ludwig Cancer Institue, 1997 — 2005.

PhD in physics, University of Munster, 1997. During PhD studies, spent three years at Vanderbilt University in Nashville.

 

The University of Reading has recently completed an £8 million BioCentre equipped with state-of-the-art instrumentation for research in genomics, transcriptomics, structural biology, proteomics and mass spectrometry. The center is currently hiring scientists for its Proteomics and Mass Spectrometry unit.

ProteoMonitor caught up with the new director of the BioCentre this week to find out about his background, and more about the center.

What is your background, in terms of research?

I did my diploma with Professor Hillenkamp and Professor Benninghofen, who is a physicist at the University of Munster. Professor Benninghofen is well known because of the SIMS methodology. So I did my diploma and also my PhD with both of these. When I did my diploma I was already starting to work on infrared MALDI. Then I went onwards and started my PhD by going a bit further into the subject and using a free electron laser at Vanderbilt University in Nashville, Tennessee. My background basically is as an experimental physicist who went sort-of astray and went medical physics, a little bit of laser physics I guess, but mainly into mass spectrometry, which was then infrared MALDI.

What did you do after you left Vanderbilt University?

I basically went back to Germany to write up my thesis. Straight after that, I went to the UK, to London and took up the post with the Ludwig Institute for Cancer Research. The main reason there was I was actually given the chance to use infrared MALDI, and this time for application purposes — to use that to look at post-translational modifications particularly — looking at phosphorylation, which is quite important for cell signaling.

IR MALDI is generally speaking softer than UV MALDI, and phosphate groups on a protein are quite labile — that is they can fall off quite quickly during the MALDI process. Infrared MALDI is softer — softer means that it doesn’t put so much energy in the bonds so that they break off. That gives you a higher probability that the phosphate group will survive attached on the protein or peptide. It’s much more likely that you see the intact phosphopeptide or phosphoprotein without knocking off the phosphate group.

What kind of discoveries did you make using IR MALDI to look at phosphorylation?

There are several things — phosphorylation on some serines, which wasn’t shown yet, and its implications. Then, we used the infrared laser to show that phosphorylation, or post-translational modification in general, would be easier, or often easier, to identify intact with an IR laser.

I didn’t do that much infrared MALDI work in the past four or five years, partially because there is a little bit of a sensitivity issue that in general infrared MALDI is not as sensitive as UV MALDI. Also, it takes a bit more time and more dedication to do IR MALDI than UV MALDI because IR MALDI instruments are less standard than UV MALDI instruments, so it’s not as easy to use as UV MALDI. Because of these reasons, I didn’t have that much time anymore to spend just on infrared MALDI.

What have you been doing in the last four to five years?

Basically, I started as a postdoc at the Ludwig Institute for Cancer Research and then went on to become a group leader there. I was then heading the group, which was later called Bioanalytical Chemistry, which basically was mainly mass spectrometry, but also had liquid chromatography and all the other analytical chemistry tools available there. I was doing a lot of analytical research for our collaborations in cancer research. I also was a collaborator in many research topics with the biochemistry department at the University College London. It was very diversified. I went from just identifying some metabolites with collaborators in physiology, all the way to identifying proteins or post-translational modifications in cancer research.

We also had a few side project with chemistry — polymerization, for instance. We did quite a lot of things. But mainly, we focused on cancer research. Because that’s what the Ludwig Institute for Cancer Research is all about.

When did you get into proteomics?

Just when I started at the Ludwig institute in 1997. That same year I was talking to a colleague of mine — another postdoc within the same group — we went after work for a pint of beer, and basically my colleague was a glycobiologist and she understood much more about biology and about the significance there. We were talking about the future, and she mentioned these new developments in proteomics and so on. For me, it caught my interest and I thought, ‘That would be cool, and that would be fantastic to use mass spectrometry for.’

What kind of problems did you start working on in proteomics?

Since I have more of this physical science and technical background, I was particularly interested in further development of the technology. What I try to do is find new ways that can actually make life easier in proteomics, mainly based on mass spectrometry. And then once we actually have new methodology, I would then try to apply this. But since I’m not the biologist, I will go back to my collaborators who are mainly from the life sciences, and then actually suggest ways to analyze their specific problem.

Have you developed significant new techniques?

We would hope so. We’ve done some things in immobilized metal ion affinity chromatography, which basically shows that we can now go down to medium- to low- fentomole sensitivity in the analysis of phosphopeptides. So immobilized metal ion affinity chromatography would be used just before mass spectrometry for separation or isolation of phosphopeptides. That way if you isolate, and get rid of background, it’s more likely that you actually detect the phosphorylated peptides by mass spectrometry.

We did a few new developments on that, which have been published. But then also, just recently what I did was use liquid matrices — which I think will have great potential in the future — I used liquid matrices for the MALDI process. As you probably know, MALDI normally is done just exclusively with solid-state matrices. So we actually have now a system that actually can give you low fentomole sensitivity with liquid matrices. This just came out in the journal Proteomics.

The other thing I’m working on on the moment is peptide derivitization. We’d like to derivitize peptides in a way that they fragment easier or better, so that you can actually use MALDI for tandem mass spectrometry by using PSD fragmentation. PSD is notoriously bad in its sensitivity, but with our derivitization, we have already shown that you can go down to 250 attomole sensitivity, and that is something, I would think, like a world record.

As you can see, there’s a lot of MALDI in my work still, and there probably will be in the future.

What’s the advantage of a liquid matrix over a solid matrix?

There are quite a few actually. First of all, a liquid matrix is probably better for quantitation if you want to use mass spectrometry. With a solid matrix, you normally have a lot of ion fluctuation if you go from spot to spot, because with MALDI you have to normally go from spot to spot when you irradiate. With a liquid matrix, you can basically just sit on one spot and irradiate there, and then that spot replenishes itself because of the liquidity of the matrix. That way you have much better consistency in the ion spectra.

Talking about consistency, this is probably kind of important for specific kinds of mass spectrometers, for example FTICR, or wherever you have some ions being trapped in a cell. There you would like to have some constant ion flux, and not something highly variable.

There are other advantages. For example, most of the solid state matrices are acidic in nature, and the liquid matrices offer another way to vary the pH and go to a less acidic pH. You could also think about online reaction monitoring. So you have your reaction going on in the liquid while you’re doing mass spec. This is not actually possible if you think about a crystalline state.

There are many of these advantages associated with the matrix itself. We’re using a glycerol based matrix, which is totally different from the acidic solid matrices.

When did you go to the University of Reading to become the director of the new BioCentre research center?

I just started here on the first of January. This is a great opportunity because you have a center at the university where you have most of the post-genomic technologies combined, like transcriptomics, array facility, DNA analysis, structural biology, X-ray crystallography. You can see that whatever happens the genome — transcribing and translating — you have the means to follow-up on the gene product.

There’s not that much in the literature comparing mRNA data with protein data. There are conflicting messages there, that the mRNA level doesn’t necessarily coincide with the protein level. That we can all analyze with the BioCentre.

You’re currently hiring for the BioCentre?

At the moment, we have a whole page ad in Nature for seven positions, or something like that, all in mass spectrometry/proteomics.

The center itself has been planned for a long time — three or four years — and it’s supposed to be an interdisciplinary hub for all people at the university and external places who would like to some post-genomic analyses. They can come to us, we can advise them, collaborate. It’s like a ‘center of excellence,’ but I would rather like to the use the term ‘interdisciplinary hub for post-genomic technologies.’

Are there specific problems researchers will be working on at the center?

I would always like to check that whoever comes to us, their research is actually feasible. Normally, people come and I tell them what can be done, and they are even more pleased because they hadn’t thought about specific ways that technology can be used. There will be this kind of collaborative aspect, but apart from that, I’m still doing technology development here which is very important for a center like this so that you always keep up to date and have always this extra bit where you’re at the forefront of science. That’s what I try to do with my own research interests.

Were you hired especially to be the director of the BioCentre?

Yes. I’ve been hired here to be the director, and I’m also heading one of the units. There are three to four units — one unit transcriptomics, and DNA analysis unit, a structural biology unit with X-ray crystallography, and then there is my unit which is mass spectrometry and proteomics. I’m the unit leader, as well as the director for the whole center.

What kind of things would you like to do in the future?

Probably something which, surprisingly, is not directly mass spectrometry related, but instead using a bit more optical detection methodologies. Once you’ve actually found out things that are biomarkers — use that information to create biosensors or biochips, which are mainly more based on optical detection methods. Also thinking about nanotechnologies and nanoparticles — this might actually be more sensitive than mass spectrometry.