Integrated Mass Spectrometry

Abstract Shared Resource 07: Integrated Mass Spectrometry (IMS-SR) The Integrated Mass Spectrometry Shared Resource (IMS-SR) provides extensive mass spectrometry services to the City of Hope Comprehensive Cancer Center (COHCCC) Members. The IMS-SR operates across both COH and TGen sites under the leadership of Dr. Patrick Pirrotte. Dr. Pirrotte is a faculty member in the Cancer and Cell Biology Division at TGen, the Department of Immuno-Oncology at COH (Beckman Research Institute), and a COHCCC Member. IMS-SR offers a comprehensive roster of state-of-the-art, yet cost-effective services built on an extensive knowledge of mass spectrometry (MS) and its applications in cancer. Specific Aims of IMS-SR: Aim 1. Provide oncology-focused, state-of-the-science MS measurement capabilities. Aim 2. Provide COHCCC Members with expert QC/data analysis and multi-omic integration. Aim3. Education, reporting, and dissemination of results. Projects initiate via interactive consultation with the IMS-SR Director and dedicated staff. The IMS-SR is structured around a proteomics unit and a metabolomics unit and houses expertise in acquiring/analyzing high- dimensional, multi-omics data in both units [i.e., (phospho)-proteomics, metabolomics, and lipidomics]. High-end instrumentation (e.g., 1x Orbitrap Eclipse, 2x Orbitrap Lumos, 1x Orbitrap Fusion, 3x triple quadrupole MS, 1x quadrupole time-of-flight, etc. totaling 11 instruments) are operated by highly trained staff with expertise in molecular and cancer biology, as well as analytical chemistry. Data acquisition is supported by robust analytical pipelines for streamlining data harmonization and integration, quality control tracking, and generating publication- quality data reports. IMS-SR also supports COHCCC investigators with incorporating their MS-based findings into grants and manuscripts. IMS-SR accelerates drug development at COH by offering cGMP services (FDA#3009323645) to characterize oligonucleotides, small-molecule active pharmaceutical ingredients, and peptide drugs. New services in high demand include targeted NAD/NAR and nucleotide profiling to dissect cancer metabolism through novel assays designed at IMS-SR. The resource also provides deep expression proteomics, proteogenomics, and extensive phosphoproteomic signaling assays, including kinome activity scoring of patient tumors to identify putative therapeutic targets. General administrative oversight is provided bi- annually by a faculty Advisory Committee and through the COH Shared Resource Steering Committee (SRSC), which meets bi-monthly. Members Utilization by %Revenue 2017–21: 72.2 Total (38 MCBC, 11.8 DCT, 10.4 CI, 11.6 HM, 0.4 CCPS) Publications by Members: 63, 18 with Impact Factor >10 Grants Supported: 45 Total (2 CIRM, 4 DoD, 1 LLS, 17 NCI of 33 NIH (26 R01))