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Excellence in Proteomics Research: A Conversation with Jeffrey Whiteaker

The following is the second entry in a new Q&A series highlighting selected Clinical Proteomic Tumor Analysis Consortium (CPTAC) researchers and their work. Join us as we discuss multiple facets of proteomics research with Jeffrey Whitaker, PhD, Director of Proteomics within the Paulovich Lab at the Fred Hutchinson Cancer Center. Transcript is edited for clarity.

Q: Could you provide a brief overview of your academic/professional journey?

JW: My academic journey began with formal training in mass spectrometry, focusing on environmental and atmospheric chemistry during my graduate studies. Transitioning to biological applications during postdoctoral work at the University of Maryland, I've spent the past 19 years at the Fred Hutchinson Cancer Center, concentrating on proteomics and biomarker discovery.

Q: Can you describe your ongoing work at the Fred Hutchinson Cancer Center? What do you find most compelling about your current projects?

JW: Currently, our lab operates as a translational proteomics hub. We're interested in taking modern proteomics discoveries and implementing them at the clinical level. That involves two main aspects. One is technology development. We’re constantly looking to make new methods that'll work and address some of the barriers that we encounter in translating proteomics. The other is in making new biological discoveries. So, discoveries that can provide new biomarkers, provide better treatment options, or reveal the mechanisms behind better treatment options for patients.

To comment on what I find most compelling about the work… the challenge of measuring proteins, especially quantifying them, is really a fascinating problem to work on because they're so complex. The opportunity to design experiments, using these state-of-the-art technologies, and working with such a diverse array of researchers, especially [the caliber] we find in the CPTAC network, it's really rewarding to… ultimately share [the results] with the scientific community. [Also] having a sense that what you're devoting your time and effort to is eventually going to help people and improve their quality of life makes what we're doing highly satisfying.

Q: With nearly two decades at the same institution, what are some factors that have contributed to your lab’s success over this period? In what ways have you seen the landscape evolve during your tenure?

JW: Stability has been a defining factor in our success. Our group here at the Hutch [has] benefited from many talented scientists that have joined and left over the years, but we've [maintained] a very stable core group of researchers... for 10 or more years together and this group is really diverse, both in backgrounds and life experiences. I think that having this core group has really been a nice aspect of our research enabling us to realize new ideas, get contributions from a lot of different people, and to manage roles, expectations, and productivity.

Over the years, working in proteomics there's been tremendous improvements in hardware and software developments for mass spectrometry-based proteomics. I think it's really been neat to see… developments on both the hardware side and the software side and how they interplay with each other… I've seen a couple of different cycles where improvements in one area have prompted a great need, and then that need is met by improvements in the other area. [That relationship] has driven the most innovative technological or scientific developments while I've been here. 

Q: As someone with extensive experience, what barriers to progress do you see in the field of proteomics today and how do you envision overcoming these challenges?

JW: If I was to outline a couple different barriers, I think in the short term… one barrier is the quality and availability of biospecimens that are available, especially for proteomics, where we're often interested in measuring post translational modifications. The ability to get quality biospecimens is something that we are currently trying to address and hopefully overcome.

In the longer term, the ability to measure, reproducibly, whole proteins. Currently, we are predominantly [using] a bottom up paradigm for proteomics. In the future, hopefully advances… made at the top down level will continue to expand our ability to interrogate whole proteins in a comprehensive manner—I continue to look forward to seeing advances in that space. To comment on barriers that I've seen socially in science… I [often see] hesitance to try new technologies in the clinic. [This reluctance] seems to be more of a social barrier where there needs to be more awareness of the benefits or a mechanism to implement new technologies in the clinical space, [more quickly].

Another barrier is reducing costs to care. Hopefully, enabling targeted personalized health care will lead to lower costs for everyone. That's something we don't necessarily work with in the research space, but I definitely see aspects where people's access to new technologies can be limited by the cost.

Q: For aspiring individuals interested in proteomics, what career advice would you offer, considering your own journey and experiences?

JW: Regardless of the field, my advice is to find something you are genuinely interested in and dedicate your time and energy to it. Passion and dedication, coupled with hard work, often lead to fulfilling careers. Surround yourself with talented individuals; science is a collaborative effort, and success often comes from teamwork. Embrace collaboration and appreciate the learning opportunities that come from working with individuals who bring diverse skills and perspectives. Remember, science is a team sport, and the journey is as important as the destination.