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Updating the MCP Proteomic
Publication Guidelines
BY ROBERT J. CHALKLEY, KARL R. CLAUSER, AND STEVEN A. CARR
Mass spectrometry (MS)-based proteomics identifies
peptides, proteins, and post-translational modifications by acquiring mass spectral data (MS and tandem
MS (MS/MS) spectra) and then analyzing the results
using database-searching software and associated statistical tools. Modern mass spectrometers allow analysis
of large numbers of components in a short period of
time, and the new instrumentation has led to an explosion in proteomic research and data production.
to be updated to reflect new experimental practices.
There was also a growing recognition that, despite the
tremendous expansion of proteomics into all aspects
of biological and clinical research, very little of the data
was being made publicly available for data mining,
comparison of methods, and software development
and refinement.
The amount of data produced is too vast to allow
manual interpretation or complete presentation, so
software is required to understand and condense the
results. Several years ago, it was realized that authors
of proteomics papers would benefit from guidelines
defining information that had to be submitted as part of
a manuscript to allow adequate assessment of reported
protein identification and analysis results.
To address these issues, a one-day meeting was
convened this past May in Philadelphia, immediately
prior to the American Society for Mass Spectrometry
annual conference. The goal of the meeting was to
produce an updated set of guidelines. The meeting,
organized by MCP Associate Editor Steven A. Carr and
editorial board members Robert J. Chalkley and Karl R.
Clauser, brought together about 25 proteomics scientists to discuss the current guideline’s weaknesses and
how the guidelines should be altered to account for new
Molecular & Cellular
experimental practices.
Proteomics (MCP) has taken
a leading role in developing
such community guidelines. In
w“as In general, there
an encouraging level
2004, an initial set of guidelines1 was drafted from discussions among members of the
journal’s editorial board. A year
later, at a meeting in Paris, a
more complete set of guidelines2 was compiled by a panel of about 30 international
experts in the application and analysis of proteomic
data. These guidelines, which have become known as
the Paris Guidelines,3 set a benchmark for assessing
proteomic manuscript content. MCP has enforced these
guidelines for all germane manuscript submissions to the
journal and other journals either recommend these same
guidelines or have their own variations.4 The guidelines
have generally been well received by the community, and
it is widely felt that they have led to an improvement in
quality and accountability of published results.
of concordance on how
To initiate debate and
set the stage for writing the
revised guidelines, attendees
spent the morning in informal
presentations that highlighted
the guidelines needed
aspects of the current guide-
lines that needed revision
and proposed new guide-
lines driven by the changes
that have occurred in the field over the past four years.
to be changed.
”
This was followed by an afternoon session in which
four breakout groups worked on rewriting the following
specific elements of the guidelines: protein identification,
post-translational modifications, quantitation, and use of
repositories.
However, as with all rapidly developing scientific
fields, new approaches and techniques are constantly being devised in proteomics. As such, it was
recently acknowledged that the guidelines needed
In general, there was an encouraging level of
concordance on how the guidelines needed to be
changed. However, two areas in particular were identified as needing discussion and reworking. The first
was quantitation data. In 2005, quantitative proteomic
analysis was in its infancy, and, as a result, it contained a very limited number of techniques. In 2009,
the research landscape is very different; quantification
information is being sought in many studies, and the
