The Noel T. Keen Hall Proteomics Core houses the following equipment and provides services as listed below.
The main technique utilizes a LTQ-Orbitrap Fusion MS coupled to 2-dimension nano-UPLC system to routinely perform MudPIT experiments. The nano-UPLC (nanoAcquity) is able to provide on-line either one-dimension or two-dimension orthogonal separation using a combination of high pH and low pH mobile phases. The LTQ-Orbitrap Fusion is an advanced MS system that integrates the functions of three mass analyzers: quadrupole, ion-trap, and orbitrap. The new Orbitrap Fusion is able to support top-down proteomics with ultra-high resolution up to 450,000. Its high sensitivity (<1 fmole) and fast scanning speed (20 spectra/sec) permit detection of low and very-low abundance peptides in bottom-up proteomics. Three different fragmentation techniques, CID, HCD, and ETD, are employed to generate MSn (n=2-10) spectra in any given experiment, and a combination of the three methods can result in the most comprehensive coverage of the proteome and protein sequences possible. ETD (electron transfer dissociation) is a very useful approach for mapping post-translational modification sites and can support studies of many types of PTM’s such as phosphoproteomics and glycoproteomics. Quantitative methods of SILAC and TMT labeling and label-free are readily available in the software control and can be applied to large-scale quantitative proteomics. Bioinformatics tools such as Mascot, Maxquant, and ProteoIQ are used to analyze MS raw data and perform database dependent protein identification.
In addition to MS data quality and analysis, experimental design is also critical in the interpretation of proteomics results. Biological conclusions drawn from proteomics research are largely dependent on how samples are treated and prepared. In order to execute scientifically and technically appropriate experiments, researchers need to have knowledge and experience in connecting the two routines: biological sample treatment and analytical chemistry. We are delighted to provide technical consultation in this regard before users set up their experiments.