Mass Spectroscopy for proteomics
Columbia University, all rights reserved.
Label-free, MudPIT, SILAC, iTRAQ
Columbia University
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.
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 g 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
Protein profiling of Drosophila, yeast, E. coli, Neisseria, mouse, human, rat
LC-MS, LC-MSMS biomarker discovery by protein sequenceing E. coli proteome
Bioinformatics, networking for quantitative proteomics
Quantitative Proteomics
Contact us
Call us at 646-558-0007
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
Supported by NYSTEM