The Core laboratories offer an extensive set of equipment and methods for most of the analytical needs within the Center. Major instruments include a GC-MS, a single quadrupole LC-MS, two tandem quadrupole liquid chromatograph-mass spectrometers, two quadrupole time-of-flight mass spectrometers, and an electrospray ion trap with electron-capture dissociation. Instrument-specific software is available on several workstations for remote data analysis. Other equipment includes off-gel electrophoresis (Agilent 3100), preparative LCs, and a flash purification system (Biotage Isolera One) for protein/peptide analyses and general sample preparation. For analysis of proteomics data, e.g., database searching and spectral counting, we have in-house licenses for Agilent Spectrum Mill, direct access to an MIT-licensed Mascot server, along with the open-source search-engine X!Tandem, and the Agilent software package Mass Profiler Professional, including Pathway Analysis, for complex MS/MS data sets for biomarker discovery or for proteomics (and metabolomics or lipidomics) projects. We also have Scaffold, from Proteome Software, that provides rapid visualization, verification, and annotation of combined results from Spectrum Mill, Mascot and X!Tandem searches. This was recently upgraded with the Q+ add-on for analysis of data from isotopically-labelled quantitative experiments (e.g., iTRAQ). In-house GraphPad Prism, SIMCA, and MatLab are available on dedicated workstations for routine and advanced statistics. Specific methods available on a routine or near-routine basis include: LC-MS/MS quantitation of etheno adducts, nucleobase deamination, aminobiphenyl-dG adducts, 8oxo-G, halogenated nucleosides, and subsequent DNA oxidation and nitration products in murine and human DNA, including simultaneous analysis of nitro-, bromo-, and chlorotyrosine; GC-MS quantitation of aminobiphenyl-hemoglobin adducts, deoxyribose oxidation products, fatty acids; enrichment of nitrotyrosine-containing tryptic peptides; MS-MS analysis of aromatic-amine-adducted peptides; peptide sequencing via tandem quadrupole, quadrupole time-of-flight or ion-trap mass spectrometry; quantitation of modified nucleobases and ribo- and deoxyribonucleosides; quantitation of N-formyl lysine from modified histones; characterization of modified ribonucleosides; enrichment and characterization of protein carbonyls arising from lipid oxidation; extraction and analysis of metabolites from tissue and fluids; selective identification and quantitation of S-nitrosothiols and other S-nitroso compounds; characterization and quantitation of corticosteroids and bile acids and their metabolites.
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