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Editor-in-Chief: |
Richard D. Smith, PhD |
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Richard D. Smith, PhD
Battelle Fellow and Chief Scientist
Biological Sciences Division
Director of Proteomics Research
Pacific Northwest National Laboratory
P.O. Box 999, 3335 Q Avenue
Richland, WA 99352 |
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Those of you familiar with Journal of Proteomics &
Bioinformatics (JPB) are well aware of the challenges underlying
research in proteomics and its associated
bioinformatics fields. These challenges—spanning experiment
design, sample preparation and processing, separations,
mass spectrometry, data processing, computational
approaches, and bioinformatics—drive some of the most
active areas of chemical, biological, and computational research
and development. As a result, experimental approaches
and knowledge are changing at an incredible pace.
New methodologies, reagents, instrument platforms, and
software tools abound — far more than even the largest
labs can realistically evaluate, and much faster than even
the most prolific researchers can track and digest, much
less adopt for the betterment of their labs. |
It’s clear in complex research areas such as proteomics
and bioinformatics, that the old ways of doing business need
to change, and indeed are changing at an increasingly rapid
pace. What’s is less clear is where these changes are taking
us and how quickly we will get there. At present the
dominant mechanism by which we disseminate scientific
advances is through peer-reviewed publications. Open access
journals such as JPB improve upon the more traditional
publication paradigms, allowing faster, free, and unconstrained
access to scientific results. This change benefits
all of us. You can help by checking out the growing
array of open access journals and seriously considering them
when you next plan to publish. |
We also need to remove biases in the review process to
encourage works that critically review and/or compare
methods and analytical approaches. While difficult and often
contentious, such publications are badly needed because
of the overwhelming amounts of information available. We may ignore or be unaware of information that could impact
the effectiveness of our labs, perhaps hoping that if something
is truly useful it will somehow rapidly gain our attention
by way of a ‘major’ publication or a news article—a
questionable hope at best. Often such information is received
second-hand, such as in a discussion or email from
colleague. This works best in fields where the research
community is small and communicates fluidly, but not so
well when the research community is large and diverse,
and where the induction period for effective dissemination
can be years.
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Are larger labs better able to discern effective advancements?
At Pacific Northwest National Laboratory (PNNL),
our proteomics program and scope of research are larger
than many. Major sources of support include the U.S. Department
of Energy’s Office of Biological and Environmental
Research, PNNL’s Environmental Molecular Sciences
Laboratory, and the National Center for Research Resources
that supports a “Proteomics Research Center for Integrative
Biology.” Our scope of research activities includes
new technology development in conjunction with a broad
range of applications. Undoubtedly the relatively large size
of our lab and research team makes it easier to consider
and explore a wide range of techniques, instrumentation,
sample processing approaches, data analysis tools, etc.
However, neither we nor any proteomics lab on earth has
anywhere near the resources necessary to broadly assess
which combination of new instrument platform(s), sample
processing and fractionation schemes, sets of informatics
tools, and so on, are most effective for each type of
proteomics application. There is no solution to this dilemma
that does not depend on the broader community. |
We are at the relative beginning of a period of profound changes in the ways in which we conduct biological research,
as well as changes to our scientific culture. As an
example, there is no doubt in my mind that the present large
scientific meetings will gradually disappear. Besides being
extraordinarily expensive, they are inefficient in the use of
researchers’ time and resources. Probably the best justification
for their continued existence is that they provide a
forum to meet with colleagues and ‘network’. At the most
recent annual conference of the American Society for Mass
Spectrometry (ASMS), which probably brings together a
larger set of proteomics researchers than any other meeting
at present, more than 6000 attendees were presented
with six parallel oral presentation sessions and nearly 700
posters per day and, if you were willing to forsake meals
(or hospitality-suite enabled networking), a wide array of
vendor sessions and workshops. |
One of the newer features of the ASMS annual conference
is that attendees can view any of the oral presentations
via the web for two months following the meeting.
My hope is this becomes common practice for all scientific
meetings, and will be extended to include meeting workshops
and perhaps even posters in some fashion. I also
hope that future meetings will offer a ‘virtual registration’ option, where, at a lesser cost, one can view the presentations
without having to physically attend. Not to offer this
option for fear that it would precipitate a drop in physical
attendance would be short sighted. But regardless, I think
such an option will turn out to be just a brief intermediate
step. While some of us likely will never want to replace
attending scientific meetings with virtual web-based conferences,
the next generation of researchers raised using“Web 2.0+” tools and who are comfortable with internet
social networking, and perhaps distributed ‘cloud science’
approaches to research, will have no such reservations. |
This brings me back to the importance of open access
literature; that is, its speed, flexibility, and unconstrained
availability. It is yet unclear what will replace the present
publication paradigm, only that something else will; the open
access movement is an early step in the right direction. I
hope you will join me in this movement, and in particular,
that you will consider using the JPB as a venue for reviews,
perspectives, and other manuscripts to communicate advances
faster and more effectively. And I expect that JPB
will continue to adapt quickly and allow us all to effectively
communicate advances faster and more usefully.
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