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Scientific Report 2007
Scripps Florida
Translational Research Institute
Proteomics Laboratory
J.A. Caldwell-Busby, V. Cavett
The
Proteomics Laboratory at Scripps Florida provides proteomics services and expertise
to scientific collaborators at Scripps Research facilities in both Florida and California,
universities within the state of Florida, and other educational institutions. We
use cutting-edge mass spectrometry technology to identify proteins, map modifications
that occur after translation, and do relative quantitation experiments with a variety
of samples.
In its lifetime,
a protein it can have several locations and functions within a cell. Location, function,
and 3-dimensional structures of proteins are all influenced by static and dynamic
chemical modifications that occur after translation. These modifications vary from
small methyl and acetyl groups, which are a part of the histone codes, to large
lipid and glycosylation modifications, which act as cellular markers and signaling
molecules. With mass spectrometry, we can detect both the small and the large changes
in mass that occur in proteins because of these modifications, and we can identify
the specific amino acids modified.
Relative changes
in protein levels between multiple samples provide biologically relevant information
about cellular pathways and proteins of interest. Large-scale studies of this type
require rigorous sample preparation and highly tuned algorithms for comparing different
mass spectrometric analyses. We are currently validating methods for both sample
fractionation and data analysis for these types of large-scale differential protein
experiments.
Mass spectrometers
at the facility include an ion-trap spectrometer, which is used mostly to identify
proteins and peptides, and a triple quadrupole mass spectrometer, which is used
for relative quantitation experiments. A new addition is a mass spectrometer that
can be used to perform accurate mass and high-resolution experiments. Each mass
spectrometer is interfaced to nanoflow electrospray ionization sources and capillary
high-performance liquid chromatography columns.
Data analysis
is performed primarily via automated workflow on a cluster maintained by the bioinformatics
group. Automation of the front-end processing allows for a more thorough review
of the resultant data and more time for development of innovative software in collaboration
with information technology groups at Scripps Research and beyond.<
Publications
Godeny, M.D., Sayyah, J., VonDerLinden, D., Johns, M., Ostrov, D.A., Caldwell-Busby, J.,
Sayeski, P.P. The N-terminal SH2 domain of the tyrosine phosphatase, SHP-2, is essential for Jak2-dependent signaling
via angiotensin II type AT1 receptor. Cell Signal. 19:600, 2007.
Sloley, S., Smith, S., Algeciras, M., Cavett, V., Caldwell Busby, J.A., London, S., Clayton,
D.F., Bhattacharya, S.K. Proteomic analyses of songbird (zebra finch; Taeniopygia guttata) retina. J. Proteome
Res. 6:1093, 2007.
Sloley, S., Smith, S., Gandhi, S., Caldwell Busby, J.A., London, S., Luksch, H., Clayton,
D.F., Bhattacharya, S.K. Proteomic analyses of zebra finch optic tectum and comparative histochemistry. J. Proteome
Res. 6:2341, 2007.
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