Multi-omics Mass Spectrometry and Biomarker Discovery Core

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Multi-omics Mass Spectrometry & Biomarker Discovery Core Facility Shared Resource ABSTRACT The Multi-omics Mass Spectrometry & Biomarker Discovery Core Facility (MMSBD) provides Cancer Center (CC) members with mass spectrometry (MS)-based multi-omics technology to support research on cancer pathogenesis, cancer biomarkers, novel anti-cancer agents, and diagnostic studies. The multi-omics approaches provided encompass high-quality MS services for proteomics, peptidomics, glycomics, lipidomics, metabolomics, and small molecule analyses. Quantitative phosphoproteomics and deep proteomics are new services provided during the current funding period. The Core offers scientific consultation from project conception and execution to preparation of manuscripts and grant applications. Primary Core services are: 1) liquid chromatographic/mass spectrometry (LC/MS); 2) untargeted/targeted proteomics, including label-free quantitative proteomics as well as stable isotope labeling with isobaric tandem mass tags or stable isotope labeling of amino acids in culture; 3) identification and quantification of post- translational modifications; 4) de novo peptide/protein sequence analysis; 5) peptide sequence validation under GMP conditions (the Core is FDA-registered); 6) lipidomics and metabolomics; 7) biomarker discovery from clinical samples; 8) assay development and quantification of small molecules, peptides, drugs, and validation of potential biomarkers; 9) tissue biomarker profiling by MALDI-MS; and 10) tissue imaging mass spectrometry. The MMSBD is well equipped with cutting-edge major instrumentation including an Orbitrap Fusion Tribrid mass spectrometer (Thermo); a 6490 Triple Quadrupole mass spectrometer (Agilent); several LC Q-TOF mass spectrometers (Waters and Agilent), and two MALDI-MS instruments. A second high-end Orbitrap mass spectrometer (a Fusion Lumos; Thermo) is being purchased to meet increased demands for LC/MS instrument time. Data analyses are performed on Core-maintained workstations and multi-node computer clusters that operate both commercial and open source software. Software is constantly updated and MS and metadata are automatically backed up and stored on several redundant storage units located on and off the main campus. The core is co-directed by Drs. Markus Kalkum and Robert Hickey, who are both faculty within Beckman Research Institute. Key decisions affecting the Core are reviewed by an Advisory Committee, composed of CC members who use the Core’s services. Since the last competitive renewal, the MMSBD contributed to 26 publications by CC members and served 73 investigators, 52 of whom were CC members representing all five Programs. Of the 52 CC members, 45 (87%) had peer-reviewed funding. Accordingly, the MMSBD provides accessible, cost-effective, and high-quality multi-omics mass spectrometry and biomarker discovery services to support the research of the City of Hope Comprehensive Cancer Center.