The Mass Spectrometry and Proteomics Core facility has the following major equipment available:

  • An Orbitrap Fusion mass spectrometer (Thermo) equipped with next generation HESI and nanoelectrospray sources, a Dionex UHPLC for high through-put metabolomics and lipidomics and an EasynanoLC for proteomics analyses.
  • A Synapt G2 HDMS high definition mass spectrometer (Waters) with ion mobility MS and nanoacquity UHPLC and a Trizaic electrospray ion source.
  • Two 6520 electrospray Quadrupole Time of Flight mass spectrometers (Agilent) for proteomics or intact protein analyses.
  • A 6490 Triple Quadrupole mass spectrometer (Agilent) with iFunnel technology equipped with a Jetstream source and an Agilent 1290 UHPLC for accurate quantitation.
  • An LTQ (Thermo) equipped with a nanoelectrospray source is available as a walkup instrument for quick nano-ESI analyses.
  • A Simultof 200 combo MALDI (Virgin Instruments) for fast and easy measurement of peptdes and proteins
  • A Simultof 300 Tandem TOF-TOF mass spectrometer (Virgin Instruments) for MS/MS analysis of MALDI ions

The Mass Spectrometry and Proteomics Core provides state of-the-art protein identification services, as well as quantitative proteomics, and analysis of posttranslational modifications. Characterization of oligonucleotides, oligosaccharides, and intact glycoproteins can be carried out by either nanoelectrospray or normal flow LCMS on the Orbitrap Fusion instrument. Relative quantitation of proteins in mixtures and cross sample comparison is performed on the Orbitrap Fusion or on the Waters Synapt G2 HDMS. Qualitative and quantitative analysis of small molecules including metabolites, lipids, peptides, and nucleosides is typically carried out on the Agilent 6490 QQQ. Protein identification with MS data is accomplished using a variety of software suites, depending on project and instrumentation. We have Sequest and X!Tandem search engines running on a 15-node computer cluster, and we have standalone Spectrum Mill, Protein Lynx Global Server, Proteome Discoverer, and Peaks Studio installed on dedicated high end computers. Proteomics data can be visualized in Scaffold. De-novo pepetide sequence analysis can be performed with Peaks Studio and protein quantitation and metabolomic data is typically analyzed with Progenesis QI, Sieve or Mass Profiler Pro. Lipid identification is performed using Thermo Lipid Search. All instrument generated data is backed up on a network-attached local storage in addition to the automatic 24/7 campus network backup routine to prevent any data loss.