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Proteotypic peptides in the spotlight Some peptides generated by the digestion of a given protein are just detected more often and more reproducibly than others. In back-to-back articles, two research groups describe their work on these proteotypic peptides. Ruedi Aebersold, Bernhard Kuster, and co-workers at the Institute for Systems Biology, Cedars-Sinai Medical Center, the University of California Los Angeles, Cellzome AG (Germany), ETH Zurich, and the University of Zurich developed a method to predict which peptides are proteotypic for a particular protein. In another study, Edward Marcotte and coworkers at the University of Texas used proteotypic peptides to determine absolute quantities of proteins in multidimensional protein identification technology (MudPIT) proteomics experiments. To predict which peptides are proteotypic for a protein, Aebersold, Kuster,
and co-workers studied the physicochemical properties of known proteotypic peptides. Large-scale, well-characterized yeast proteomics data sets that were generated by four common proteomics platforms (1DE/ESI, 1DE/MALDI, MudPIT/ESI, and MudPIT-ICAT) were studied. A total of 494 physicochemical properties, such as charge, likelihood of forming secondary structures, and hydrophobicity, were assessed. The properties that best predicted whether a peptide would be proteotypic varied according to platform. The predictors for yeast also correctly predicted proteotypic peptides for a human data set. The researchers estimate that with their predictors, at least one proteotypic peptide can be identified for most yeast and human proteins. In the other study, Marcotte and coworkers developed a method for largescale absolute protein expression (APEX)
measurements on MudPIT data. No labels and no added standards are necessary. The algorithm estimates the concentration of a protein in a sample on the basis of the number of its peptides that are detected. Factors such as ionization efficiency and amino acid composition are used by APEX to correct for the fact that some of a protein’s peptides are not proteotypic and will not be detected. After the correction is made, the fraction of peptides contributed by a protein to the injected sample pool becomes proportional to the fraction of its peptides that are observed in the MudPIT experiment. The protein abundances calculated with APEX correspond to known abundances over ~2.5 orders of magnitude, and correlate well with data obtained with other approaches. (Nat. Biotechnol. 2007, 25, 117–124)
PEOPLE Sweedler named associate editor Jonathan V. Sweedler
with the neuroscience and bio-
ested in the roles that such neuromodula-
is the newest associate
engineering programs.
tory compounds play in behavior, learning,
editor of Analytical
Sweedler conducts research
and memory.
Chemistry. He was al-
in bioanalytical chemistry and fo-
ready serving as an ac-
cuses on the development of ana-
from the University of California Davis in
tive member of the
lytical methods for assaying com-
1983 and his Ph.D. from the University of
journal’s editorial advi-
plex microenvironments. Those
Arizona in 1989. After a postdoctoral fel-
sory board when his
techniques involve CE, laser-
lowship at Stanford University, he joined
new appointment took
based detectors, MALDI sampling
the University of Illinois faculty in 1991.
effect on March 1.
techniques, nanoliter-volume
Among the prizes that he has been award-
Sweedler earned his B.S. in chemistry
Sweedler is the William H. and Janet Lycan
NMR, and micro- and nanofluidic sam-
ed are the Heinrich-Emanuel Merck Prize
Professor of Chemistry and director of the
pling. His group applies these methods to
(2002), and the American Chemical Society
Roy J. Carver Biotechnology Center at the
studies of the distribution, metabolism, and
Division of Analytical Chemistry’s Award in
University of Illinois at Urbana–Champaign.
dynamic release of neuropeptides and
Chemical Instrumentation (2002) and
In addition, he is a faculty member of the
classical neurotransmitters in a cell-spe-
Arthur Findeis Award for Young Analytical
university’s Beckman Institute for Ad-
cific manner as well as the roles of neuro-
Scientists (1997). The American Associa-
vanced Science and Technology and Insti-
transmitter cotransmission in well-defined
tion for the Advancement of Science elect-
tute for Genomic Biology and is affiliated
neuronal networks. He is especially inter-
ed him a fellow in 2001.
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news
PEOPLE 2007 ACS national award winners
From left to right: The 2007 ACS national award winners included Michael D. Fayer, Jean H. Futrell, James W. Jorgenson, J. Michael Ramsey, and George M. Whitesides.
Among the honors presented on March 27 at the 223rd American Chemical Society (ACS) National Meeting and Exposition in Chicago were: Michael D. Fayer won the E. Bright Wilson Award in Spectroscopy for his work in nonlinear optical spectroscopy. Fayer is the David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry at Stanford University. The prize recognizes numerous contributions that include the transient grating and photon echo techniques and ultrafast IR vibrational echo experiments. Jean H. Futrell earned the Frank H. Field and Joe L. Franklin Award for Outstanding Achievement in MS, which is sponsored by Waters Corp. Futrell is currently a Battelle Fellow at the Pacific Northwest National Laboratory. His contributions include tandem MS, including the triple quadrupole; mechanisms and dynamics of low-energy ion– molecule reactions; the ion funnel; and the understanding of fundamental ionic phenomena such as collisional activation and energy transfer of ions at surfaces. James W. Jorgenson won the ACS Award in Analytical Chemistry, which is sponsored by the Battelle Memorial Institute. Jorgenson, a former associate editor of Analytical Chemistry, is the William Rand Kenan, Jr., Distinguished Professor of Chemistry at the University of North Carolina at Chapel Hill. The 2606
award recognizes his impact on the field and on society with the development of CE, which made rapid sequencing of the human genome possible, as well as ultrahigh-pressure LC, multidimensional separations, and single-cell analysis. J. Michael Ramsey received the ACS Award in Chromatography, which is sponsored by Supelco, Inc. He is the Goldby Distinguished Professor of Chemistry at the University of North Carolina at Chapel Hill and a former editorial advisory board member of Analytical Chemistry. Ramsey is best known for his work in lab-on-a-chip technology
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and nanofluidics, and he has made contributions in MS. George M. Whitesides received the Priestley Medal, which is sponsored by ACS, and recognizes distinguished service to the chemistry community. He is the Woodford L. and Ann A. Flowers University Professor at Harvard University. His research interests range quite broadly, but he currently emphasizes areas such as physical and organic chemistry, materials science, surface science, microfluidics, self-assembly, micro- and nanotechnology, and science for developing economies.
Analytical chemist wins Grainger Challenge Abul Hussam, a chemistry professor at George Mason University, won the National Academy of Engineering’s Grainger Challenge Gold Award ($1 million) for his household system for removing arsenic from drinking water. Hussam earned his B.S. and M.S. in chemistry at the University of Dhaka (Bangladesh) and his Ph.D. in analytical chemistry from the University of Pittsburgh. The prize was meant to encourage the development and dissemination of technologies to enhance social and environmental sustainability. Water For People won the Silver Award ($200,000), and the Children’s Safe Drinking Water Program at Procter & Gamble Co. earned the Bronze Award ($100,000). In Hussam’s approach, water passes through a bucket filled with river sand, which removes coarse particles, and 20 lb of a composite iron matrix, which removes inorganic arsenic. Then the water flows through a second bucket filled with coarse river sand, wood charcoal (to remove organics), and fine river sand and wet brick chips (to remove fine particles and stabilize the fluid flow).
