Columbia University, all rights reserved.
Quantitative Proteomics Center
Department of Biological Sciences
Our Synapt G2 QTOF mass spectrometer with ion mobility separation and NanoAcquity UPLC (Waters Corp.) allow us to implement label-free protein profiling, a leading technique in quantitative discovery proteomics for systems biology and biomarkers. Drosophila, yeast, E. coli, Neisseria, Nitrosomonas, mouse, rat and human and viral proteomes have been studied in our lab.
References
1.        W. W. Wu, G. H. Wang, S. J. Baek, R. F. Shen, Journal Of Proteome Research 5, 651 (Mar, 2006).
2.        J. C. Silva et al., Molecular & Cellular Proteomics 5, 589 (Apr, 2006).
3.        J. P. C. Vissers, J. I. Langridge, J. Aerts, Molecular & Cellular Proteomics 6, 755 (May, 2007).
4.        D. M. Xu et al., Molecular & Cellular Proteomics 7, 2215 (Nov, 2008).
5.        J. C. Silva, M. V. Gorenstein, G. Z. Li, J. P. C. Vissers, S. J. Geromanos, Molecular & Cellular Proteomics 5, 144 (Jan, 2006).
6.        F. Y. Cheng, K. Blackburn, Y. M. Lin, M. B. Goshe, J. D. Williamson, Journal Of Proteome Research 8, 82 (Jan, 2009).
7.        X. F. Wang et al., Developmental Cell 15, 220 (Aug, 2008).
Label-Free Shotgun Proteomic Profiling
Label-free quantitative protein abundance data from adult human stem cells shows distinct pattern of expression in cluster analysis
We use splitless nanoflow chromatography coupled with quadrupole time-of-flight (QTOF) mass spectrometry to determine proteins quantities in cells, tissues,  subcellular fractions and affinity fractions, biofluids (serum, plasma, urine and saliva proteomics).  Ion mobility separation adds a multidimensional (2D) separation based on shape and cross sectional area of peptides in addition to mass/charge ratio. 

In one study of protein levels in a model system for apoptosis and regeneration in the mouse olfactory epithelium we found differences in protein levels for numerous proteins in the comparison of treatments affecting these biological processes. The validity of these results and the overall utility of this technique were demonstrated by the fact that five already known markers of these processes were confirmed by this technique and a number of new proteins were discovered as differentially expressed.

In another study with E. coli we confirmed differential regulation of several proteins already detected by the DIGE technique and other methods, and also found new differentially-regulated proteins in this gene knockout experiment.
Innovations
Recent innovations in this area have demonstrated a variant of the label-free approach in which mass spectra are recorded at alternate low (precursor) and high (product) fragmentation voltages in a method called MSE (2).  In this approach rapidly alternating parent and product ion spectra are generated in a protocol that seeks to record "all the ions all the time,  and these data are analyzed with an ion accounting algorithm. Increases in reproducibility of chromatographic separations have enhanced the feasibility of this approach.  Building on these conceptual and instrumentation advances a number of groups have demonstrated effective use of this method for microbial cells (2), human serum (3), and cancer cells (4). Waters Corporation (Milford, MA) has implemented the MSE algorithm in a software routine known as IdentityE.  We have used this system to study proteomes of Drosophila, yeast, bacterial (E. coli, Neisseria, Nitrosomonas), mouse, rat and human proteomes.
Synapt, MSE, IdentityE, Mass spec for serum, plasma, cell and tissue culture proteomics
We use two complementary techniques to compare different proteomes or compare affinity purifications and immunoprecipitates.  The first is label-free shotgun protein profiling as described here.  Another technique called difference gel electrophoresis (DIGE) is also described in this website (click here).
Background in Quantitative Proteomic Analysis
Early approaches to quantitative proteomics used a comparison of 2-dimensional electrophoretic gels (2D gels) coupled with mass spectrometry, then progressed to the use of isotopic labeling (e. g. ICAT, iTRAQ, SILAC) in a shotgun liquid chromatography/mass spectrometry (LC-MS and LC-MSMS) strategy, or the use of fluorescence labeling in gel-based proteomics (1).  All of these approaches have some limitations. The gel-based approaches tend to be cumbersome to use, place restrictions on experimental design and address a limited subset of proteins. The isotopic methods also place stringent limits on experimental design, the type of samples that may be analyzed, and often rely on weak isotopic signatures. Protein arrays are at an early stage of development. Finally, targeted (multiple reaction monitoring mass spectrometry) analyses address a limited pre-determined selection of proteins and can be expensive to implement.  Consequently, there is increasing interest in using so-called "label-free  methods to make proteome-wide comparisons. This technique is an ideal discovery tool for understanding biological processes, stem cells, developing biomarkers for a variety of uses,
comparing affinity purifications and immunoprecipitations and studying biofluids such as urine, saliva, plasma and serum.
Our Results
LC-MS proteome quantitation for stem cell biomarkers shotgun LC-MSMS