Proteomics researchers come from all sorts of backgrounds: analytical chemistry, biology, biochemistry, physics, genetics. But you'll never hear a proteomics researcher say, "I have a degree in proteomics." Or will you?
Actually, you will. Or at least in Europe. There, proteomics education seems to be headed in a more formal direction, with classes, mini-courses, and even year-long degree programs being offered on the subject.
But the courses, and especially the degree programs, raise the question of whether specialized, narrowly focused education and training will lead to a better breed of proteomics researchers, or whether that kind of training is destined to grow stale very quickly in the face of unyielding technological development.
The most recent example of this trend comes from Switzerland, where the University of Geneva this month will graduate its first batch of students from its Master's in Proteomics and Bioinformatics program, a three-semester program that includes nine mandatory courses, a few optional courses, and one semester of practical training.
"[The program] evolved naturally from the experience and networking of the people working in Geneva," said Patricia Palagi, the coordinator of the Master's program who is also a senior scientist in the Proteome Informatics group at the Swiss Institute of Bioinformatics. "For more than 20 years, Dennis Hochstrasser, Amos Bairoch, Ron Appel, Robin Offord, and other key names in proteomics and bioinformatics have been working together in the Geneva area. It was most natural to join forces and put together a Master's program."
"For more than 20 years, Dennis Hochstrasser, Amos Bairoch, Ron Appel, Robin Offord, and other key names in proteomics and bioinformatics have been working together in the Geneva area. It was most natural to join forces and put together a Master's program."
Nine students enrolled in the first year of the Master's program, and 23 students have enrolled in the second year. All of the students had just finished their Bachelor's degree, Palagi said.
In addition to the University of Geneva, the University of Science and Technology in Lille, France, offers a Master's program in proteomics. The program includes about 300 hours of mandatory lecture courses, mandatory and optional laboratory courses, and a six- to eight-month internship.
Meanwhile, in the United States, it is uncommon to find whole courses dedicated to proteomics, let alone degree programs or tracks in proteomics. Proteomics researchers that ProteoMonitor spoke to all said that they knew of no degree programs in the US for proteomics.
"I'm envious that they can pull together the resources to pull that off," said Joseph Loo, a professor at the University of California, Los Angeles, when he learned this week from ProteoMonitor of the University of Geneva's Master's program. "I certainly do think in the US that the interest level is there, but it would really take resources to construct a course curricula like that.
"It would probably be something where several faculty from several universities would have to get together to put together the curriculum," he said. "I'm not aware of too many funding agencies that would fund such an effort, but it might be something that we just have to suggest to them to consider."
Loo heads UCLA's mass spectrometry and proteomics core facility, and started teaching the university's only course on proteomics five years ago.
"Proteomics is a hard target to put under one course, or several different courses, because it evolves every year. It rapidly evolves to include a lot of other things," he said. "I haven't found a suitable textbook that I can recommend for my students for my class. Often I talk about papers that are just being published as I'm coming to class."
While the University of Geneva offers separate courses on bioinformatics, protein profiling, protein expression and interaction, protein post-separation analysis, proteomics applications, structural bioinformatics, statistics and probability, and more, Loo crams 2D gels, mass spectrometry and chromatography, protein interactions, bioinformatics and data analysis, biomarker discovery and new methods such as protein arrays all into one semester-long lecture course.
"One could easily have a five- or 10-week class on each of the topics I teach," said Loo. "But we've kept it broad. If, in the future, we decided we needed more focused classes, we could develop them, but we have a lack of faculty that can teach these classes, or that have an interest in these classes."
"I certainly do think in the US that the interest level is there, but it would really take resources to construct a course curriculum like that."
According to Palagi, the fact that the US does not have larger educational programs in proteomics does not reflect a lack of resources, but rather a difference in educational philosophy.
"It is probably a question of philosophy, because there are many [resources] in the US," said Palagi. "I would say that Europeans are less afraid of trying new things."
Broad vs. Specific Education
Some proteomics researchers believe that it is not necessary to have focused education in proteomics, and that it is better to keep education broad.
"I worry about training students too narrowly, frankly," said Michael Snyder, a professor at Yale whose research focuses on genomics and system biology, as well as proteomics. "Science changes. We're not training them for the next five or 10 years; we're training them for the next 40 or 50 years."
Snyder said that proteomics is an important component of research, but having a degree-granting mechanism in the subject is not essential.
"I do like to think bigger," he said. "Harvard is setting up a systems biology program, and that makes more sense to me."
At Yale, there are no courses dedicated solely to proteomics, but the field has become a significant portion of a course called "Genomics and Bioinformatics," that is offered to undergraduates and first- and second-year graduate students, Snyder said.
In addition, a few proteomics techniques have made their way into biochemistry laboratory courses at Yale, and students can do independent study under the mentorship of proteomics researchers at the university, Snyder added.
At Harvard and Cornell University, the situation is similar. Proteomics is not offered as a course on its own, but it has found its way into various other courses, including courses in biology, biochemistry, post-genomics, biomedical engineering and plant biology.
"I think the technology's really powerful, and I'm very heavily invested in it, but whether I think it should be part of the basic curriculum is another question all together," said Joshua LaBaer, a founder and director of the Institute of Proteomics at Harvard Medical School.
LaBaer, who teaches a two-week course in proteomics at Cold Spring Harbor every year, said that it could be a good idea to offer a one-semester graduate course in proteomics at Harvard, especially given that the CSHL course is very popular.
"On average, we take one out of every six applications we get for the [CSHL] course. It's very hard to get into the course, actually," said LaBaer. "The advantage to teaching more of [proteomics] is that it would allow people who might not have thought about it to think about it in the context of their own experiments. I think a lot of people could benefit from its application, if they only knew it existed, or if they only knew how it could be used."
However, LaBaer agreed with Yale's Snyder that students should not be taught too narrowly.
"Technologies come and go. You'll find that the hottest, latest thing in proteomics is now considered passé, and people are already thinking about experiments in a very different way now," he said. "What you want to do is impart a broader education about how proteins behave, what methodologies exist for measuring proteins, and the fundamentals about how those technologies work."
University of Geneva's Palagi agreed that a broader education is sometimes better than a specific one. However, a specific education in combination with a broad one is not a bad idea, she said.
"Since students have already had a broader education during the three-year Bachelor's program, why not try to be more specific during the Master's program?" she said. "Anyway, I would not call a mixture of proteomics and bioinformatics a 'specific' education."
Kelvin Lee, an associate professor at Cornell whose research focuses on proteomics, said that both depth and breadth of knowledge are critical for proteomics researchers.
"The field is multidisciplinary by nature," he said. "People with depth of knowledge in various disciplines work together on a particular problem and it would be nearly impossible for a single individual, in the context of a degree program, to gain enough knowledge in all of the respective disciplines to make contributions by themselves. … On the other hand, like much of modern biology, the field requires individuals to have a breadth of knowledge across disciplines to foster communication with people from other disciplines."
— Tien-Shun Lee ([email protected])