Mass Spectrometry and Tandem MS/MS
Instrumentation and Services Available
An ABSciexTripleTOF 5600+, an ABSciex 5800 Proteomics Analyzer (MALDI TOF-TOF), a Waters Synapt HDMS with Ion Mobility capacities, an MDS-Sciex 4000 QTrap, and a Voyager DE-PRO (Perseptive Biosystems) are available for analyses of protein, peptide, lipid, small molecule, and oligonucleotide samples. Analysis of digests of highly complex mixtures, such as whole cell lysates or serum proteins, commonly yield identification of 600-6000 proteins from single samples, & identification of proteins purified by column chromatography, by metal affinity chromatography, by gel electrophoresis, or from PVDF/nitrocellulose membranes are also available, e.g., detection of phosphoproteins and other post-translational modifications, isozyme analysis, & identification of disulfide bonds.
Additional analysis such as metabolite ID, Lipid ID, or targeted protein ID/quantitation using peptide MRMs are also available.
Discovery quantitation of differences in protein amount between samples can be done by in vivo SILAC metabolic labeling or iTRAQ isotope tagging post-harvest (up to 8 separate samples with 500-2500 proteins ID'd and quantitated in single experiments), or by MS identification of spots of interest on 1D/2D gels. For quantitation of lists of pre-determined proteins of interest, peptide SRM (MRM) assays can be developed to allow rapid sequential relative or (with heavy isotope peptide standards) absolute quantitation of proteins of interest. Finally, combined ID and label-free quantitation ("Qual/Quant") analyses can be performed using Data-Independent Analysis (DIA) SWATH methods