Michael Washburn on the Development and Applications of MudPIT

Scientist Interview: July 2011

Michael Washburn

Recently Essential Science IndicatorsSM from Clarivate Analytics named Dr. Michael Washburn a Rising Star in the field of Molecular Biology & Genetics. His current record in this field includes 51 papers cited a total of 2,329 times between January 1, 2001 and February 28, 2011. He is also among the top 1% of researchers in the fields of Biology & Biochemistry, Chemistry, and Microbiology.

Washburn is the Director of the Proteomics Center at the Stowers Institute for Medical Research in Kansas City, Missouri. He is also an Affiliated Associate Professor in the Department of Pathology and Laboratory Medicine at the University of Kansas School of Medicine.

BELOW, SCIENCEWATCH.COM CORRESPONDENT GARY TAUBES TALKS WITH WASHBURN ABOUT HIS HIGHLY CITED WORK.


SW: Your educational background is in biochemistry and toxicology, how did you end up with a research program dedicated to protein mass spectrometry?

I got my Ph.D. in biochemistry and toxicology at Michigan State University. It was after I actually finished my degree, I still had no idea of what I wanted to do, when I heard a series of lectures by Fred McLafferty, a long-standing senior person in mass spectrometry, a member of the National Academy of Sciences. He was talking about how mass spectrometry can be used to detect really tiny amounts of things. I thought it sounded cool and I started looking at post-docs in proteomics, wanting to do mass spectrometry. That was maybe the fall of 1998.

I ended up doing a post-doc with John Yates at the University of Washington, which is where we really got started developing new techniques for looking at proteins using protein mass spectrometry. John moved to San Diego and I went with him and worked at a company there that no longer exists, called the Torrey Mesa Research Institute, where we continued our method development research. John also has an academic laboratory at the Scripps Research Institute, which is where he continues his research.

The work started in Washington continued in San Diego, and it led to the further development of novel and powerful proteomics technologies. We called it MudPIT, and it really had a huge impact, just an enormous impact on the field.

SW: What does MudPIT stand for and how does it work?

It stands for Multi-dimensional Protein Identification Technology and it is a chromatography-based approach for looking at complex protein mixtures. You can basically digest proteins, load them directly onto a column, and place the column directly in line with the mass spectrometer. At the end of the day, what you get after doing some database searching and analysis is a list of all proteins that came from the original mixture.

Nowadays people are mostly using it to study protein complexes, and they can also get really strong quantitative information out at the same time. So you can know not only what's present in the original mixture, but how much of it is present.

SW: Would you describe your expertise in protein mass spectrometry in the technology itself or in the application of the technology to real-world problems?

It used to be very technical, but now it's in the biological application of it.

SW: When would you say the MudPIT technology was actually perfected for use?

"A multidimensional protein identification technology (MudPIT) stage coupled to an ion trap mass spectrometer"
"A multidimensional protein identification technology (MudPIT) stage coupled to an ion trap mass spectrometer"

We probably still haven't, I'm sure. Some things never end. The whole technology has just continued to improve, year after year.

SW: Your highest-cited paper, with a couple of thousand citations, is the 2001 Nature Biotechnology article, "Large-scale analysis of the yeast proteome by multidimensional protein identification technology," (Washburn MP, Wolters D, Yates JR, 19[3]: 242-7, March 2001). Was this the description of MudPIT, and why yeast?

Yes, that's the description of MudPIT. And we studied yeast because it was cheap and easy. That's really the truth. It's the simplest thing to grow in quantity; you get plenty of protein, and so it wasn't a problem wasting it as we tried to improve our methods. It's much more cost effective than anything else. And the yeast community had done so much of the basic biochemistry and cell biology that it was particularly easy to do a good job interpreting the data. But the reason this paper is so highly cited is not because of what we learned about yeast but because of the technology we were using and describing.

SW: Are you surprised at the impact it's had, how highly cited this paper has become?

Well, to say that I was stunned to learn how well these papers have done would be an understatement. My first instinct was this can't be right. But now it makes sense to me. One thing I did know is that we've helped change the way people think about protein mass spectrometry and that's pretty rewarding.

So now it makes sense, but years ago, when I was doing the work, I had no idea this would happen. I had a strong sense, as a lot of others did, too, that we had to get away from the two-dimensional-gel approach everybody was using and into chromatography. That paper and other papers from other labs played a role in changing people's thinking on this. At the time, though, I thought it was cool and powerful, but I had no idea it would play out as it did.

SW: If you were to write that paper again, would you do anything differently? Include anything you didn't include originally?

Probably not. I think we did the right things back then. It was what the field needed.

SW: Your second most-cited paper is the 2001 article in Analytical Chemistry, "An automated multidimensional protein identification technology for shotgun proteomics," (Wolters DA, Washburn MP, Yates JR, 73[23]: 5683-90, 1 December 2001). Is that just a companion piece to the Nature Biotechnology article?

Very much so. The Nature Biotechnology paper describes more about the information we captured. The Analytical Chemistry paper gets more into the technical details of how it was captured. And Dirk Wolters and I really worked really well together. He deserves as much credit as I do, as do others as well. We made a very good team.

SW: When did you move to the Stowers Institute in Kansas City, and was it difficult for a young researcher to commit to such a new institution?

We came here in the summer of 2003. I'm a mid-westerner by nature and nurture, and I had been to Kansas City before. I'd gone to Arrowhead Stadium when I was in college to see a Rolling Stones concert. What drew us here, the main thing, though, is that we had a lot of resources to set up this technology. Mass spectrometers are expensive. That was the great thing that Mr. and Mrs. Stowers did when they set up this Institute. They were willing to invest in resources, even for someone like myself who was basically at an assistant-professor level. They were making an incredible investment in us, and that turned out, fortunately, really well.

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