The Mass Spectrometry and Proteomics Core facility has the following major equipment available:
The shared mass spectrometry facility includes one Thermo Finnigan LTQ-FT linear ion trap/ion cyclotron resonance mass spectrometer, two Agilent 6520 electrospray Quadrupole Time of Flight mass spectrometers for high throughput proteomic analyses and an Agilent 6410 Triple Quadrupole mass spectrometer for accurate quantitation, to be replaced in the near future with an Agilent 6490 Triple Quadrupole with iFunnel technology and UHPLC. The core has recently added a Waters Synapt G2 HDMS high definition mass spectrometer with ion mobility MS and nanoacquity UHPLC for high through-put proteomic, lipidomic and metabolomic analyses. Available to the core facility are a Thermo Finnigan LCQ-Deca mass spectrometer equipped with a vacuum MALDI source and a Thermo Finnigan LCQ classic equipped with a nanoelectrospray source. In summary, the Mass Spectrometry and Proteomics Core can now provide protein identification by top-down and bottom-up (utilizes enzymatic digestion to reduce whole proteins into peptides) methods. Additionally, oligonucleotide, oligosaccharide, and intact glycoprotein characterization can be carried out using either nanospray or LCMS using the LTQ-FT. Relative quantitation of proteins in mixtures and cross sample comparison can be achieved easily on the Waters Synapt G2 HDMS. Qualitative and quantitative analysis of small molecules can be carried out, including metabolites, lipids, peptides, and nucleosides. Protein identifications from MS data is accomplished using Sequest or X!Tandem search engines running on a 15-node computer cluster, or with standalone Spectrum Mill or Protein Lynx Global Server. Metabolomics data is analyzed with XCMS or MarkerLynx and Mass Profiler Pro is to be acquired shortly. All data is backed up on two duplicate hard drives over the network in addition to the automatic 7x24 campus network backup routine to prevent any data loss.