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Quantitative Proteomics and Metabolomics Center
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 (clinical) and viral proteomes have been studied in our lab.
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 Orbitrap or 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 other methods, and also found new differentially-regulated proteins in this gene knockout experiment.
Shotgun proteomics is a strategy with broad applicability using liquid chromatography-mass spectrometry (LC/MS). The method of choice for data collection has long been a data-dependent acquisition (DDA) method in which acquisition parameters are modified in real time by selecting a narrow mass window in a quadrupole analyzer for precursor ion selection  for fragmentation after an initial survey scan. More recently, a strategy has been implemented using data-independent acquisition (DIA) in a method called MSe on the Waters quadrupole time-of flight platform to perform data collection in a massively parallel method rather than selecting single masses sequentially.
We now also collect DIA data on our new Thermo Orbitrap Q Exactive HF platform and analyze with Spectronaut software (Biognosys AG) with HRM calibrants added and spectral library generation. These robust and flexible platforms allow the design or large analyses of clinical patient samples, cell culture or animal model experiments without the stringent restrictions on experimental design imposed by isotopic labeling.
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.  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
New state-of-the-art Orbitrap QExactive HF mass spectrometer (Thermo Scientific) with resolution 240,000 and 18 Hz scan speed. Supporting that instrument is an RSLCnano UPLC also from Thermo Scientific. This system allows extraordinarily deep proteome searches as well as intensive studies of post-translational modifications