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Quantitative Proteomics and Metabolomics 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 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 to perform these comparisons.
The focus of the Center is the
identification of proteins and metabolites 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 with a strong focus on stem cell science.
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 equally with academic and industry partners
leading to new funding and scientific opportunities.
Background - Quantitative Discovery Proteomics by Mass Spectrometry
Practical Systems Biology Approach to Quantitative Proteomics Widely Applicable
While we follow many approaches, we emphasize label-free profiling technology that offers -
< Flexible experimental design with no limits on numbers of treatments and replicates - providing high statistical power
< No need for the expense of costly isotopically labeled amino acids that increase the economic risk in sample preparation
< Simple experimental protocols in which the chemistry does not restrict the experimental design of the biology component of the experiment
< Easy application to patient samples or affinity pull-downs