The Proteomics Pedigree

When Michael MacCoss started his proteomics lab at the University of Washington a few years ago, he discovered that he had been assigned his postdoc advisor's old lab space. "[It] was actually pretty intimidating," he says.

Small wonder: MacCoss' former PI was proteomics great John Yates, who ran a lab at Washington for eight years before heading to the Scripps Research Institute.

Yates, who began his career studying "protein sequencing using tandem mass spectrometry," did his own postdoc at Caltech with a high-profile PI: Lee Hood. When Hood moved to the University of Washington and started the molecular biotechnology department, he offered Yates a faculty position.

Yates recalls that being a newbie in Hood's star-studded department meant not being a top pick for students. The department had "fairly famous faculty," he says, "and if the students had half a brain they went to work with those guys." He began his lab with several postdocs and a single student, a pattern that has continued throughout his career. "I only ever had one student at a time," he says. "I've come to call it Jedi knight training."

If that's a reflection of quality over quantity, Yates' postdocs say they're grateful for the high-quality lessons they learned during their time in his lab. Ashok Dongre, now an associate director at Bristol-Myers Squibb, remembers that Yates was a "hands off" manager. "He gave a broad idea of what he wanted," Dongre says, "and he gave us the latitude to go ahead and try different things." He adds that he found the environment so rewarding that he's fostered the same atmosphere in his own lab ever since.

In fact, Yates says that this trait was an inheritance for him as well. He remembers his PhD advisor being "really good about … letting me explore ideas in the lab," he says. "That's something that I brought to my lab." Yates says a quality he really values in his lab members is being vocal and willing to speak their minds.

Dongre says what impressed him most about Yates was his refusal to follow the path that most people were taking if it didn't make sense to him; he was known among his staff as someone who carved out his own path. When he had an idea that didn't match up with what most other proteomic scientists were doing, Dongre says, Yates would analyze "the pros and cons of what he was proposing and say, 'There's a good chance that we'll fail at this, but that shouldn't stop us from trying it out.'"

MacCoss remembers that Yates "always really liked those aggressive, high-risk ideas" — a characteristic that encouraged his students to conduct research as innovative and unique as his own. "[What] you learn from being in John Yates' lab is thinking big," MacCoss says.

But it's not all blue-sky science. Yates says he's a stickler for making sure his students learn the instrumentation inside and out. "The key for them is to learn as much about the technology as they can," he says. In his lab, everyone's required to "run their own samples and maintain the instruments."

MacCoss says that for him, one of the major lessons he learned early on was the importance of software for processing proteomics data — no one going through the Yates lab was going to emerge without a real appreciation for, and grasp of, good analysis procedures. "That's something you learn right off the bat — you're not going to be able to sit there and process all your data by hand," he says.

Both MacCoss and Dongre say they've kept in touch with Yates, who has been very supportive of his postdocs as their careers unfold. MacCoss says, "I remember the first couple grants I was writing, and I was getting bad reviews." He would send the proposals to Yates for feedback, and "he was always very positive with his comments," MacCoss says.

That candor (along with a dry sense of humor) is something Yates' students know well, says Dongre. "The thing I liked about him was that I always knew where I stood with him," he says. "If he doesn't like something, he'll tell you so."

Naming Names

As one of Lee Hood's postdocs, John Yates is no stranger to a high-profile pedigree. The students and postdocs who have gone through his lab have also parlayed their experience into successful careers. To name just a few:

Ashok Dongre
After his postdoc with Yates, Dongre packed up for Bristol-Myers Squibb, where he is currently an associate director.

Laurence Florens
As managing director of proteomics at the Stowers Institute, Florens was awarded the Hudson Prize in recognition of innovative research in 2006.

Michael MacCoss
MacCoss runs a mass spectrometry lab at the University of Washington, and was named one of the up-and-coming scientists in Genome Technology's 2006 Tomorrow's PIs issue.

Michael Washburn
Washburn continues his work in quantitative proteomics, and serves as proteomics director at the Stowers Institute. Along with Florens, he won the Hudson Prize in 2006.

Christine Wu
An assistant professor of pharmacology at the University of Colorado, Wu works with membrane proteins and biomarker profiling, as well as improvements of proteomics
methods.

Fuquan Yang
Yang works on quantitative proteomics and protein dynamics as a professor at the Chinese Academy of Sciences' Institute of Biophysics.