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Quantitative Proteomics Center
The proteome is the expressed
protein complement of a cell, matrix, organelle, tissue, organ, or
organism. It includes all isoforms and posttranslational variants
and varies with time. The overall technical approach in proteomics was
enabled by two major technical advances: the ability to fully sequence
genomes and the ability to analyze proteins by mass spectrometry.
Comparative and quantitative proteomics defines the differences
in expression of proteins among different biological states (e.g.,
control vs. treatment, healthy vs. disease, specific genotype vs. wild
type) or for affinity purifications. The Department of Biological
Sciences of Columbia University has established the Comparative
Proteomics Center to apply these emerging technologies to a wide range
of biomedical research studies. We use label-free shotgun profiling with LC-MS as well as 2D gel-based techniques to perform these comparisons.
The focus of the Quantitative
(Comparative) Proteomics Center is the identification of proteins with
differential quantitative expression in cells, tissues or in affinity
purifications, and we have applied this technique employing mass
spectrometry to many different research problems.
The shotgun
proteomics label-free method provides protein abundance, fold change
ratios, P-values for adult-derived human stem cells (n=9). Agglomerative
hierarchical cluster of Z-score transformed intensity data (above)
illustrates differential expression (see our paper in J. Proteome Res.,
2011, 10 (7): 3050-3059).
A wide variety of proteomes can be
processed including cells, tissues, organelles, biofluids, affinity
preparations, and pull-downs. Bacterial, yeast, insect and
mammalian proteomes have been effectively studied. With low µg
amounts of material we can create a complex profile of quantitative
relative expression for almost any biological system. Accurate
mass and retention time data allows mining of large datasets for unique
biological insights based on large-scale protein profiling.
We do projects with groups at
Columbia University and at other institutions across the nation. All
internal and external research groups are treated equally. We
welcome collaborations leading to new funding opportunities.
Background - Quantitative Discovery Proteomics by Mass Spectrometry
Practical Systems Biology Approach to Quantitative Proteomics Widely Applicable
