Proteomics Shared Resource

PROTEOMICS SHARED RESOURCE: ABSTRACT Characterization and quantitation of proteins at both the single protein and proteome levels are critical to advancing the understanding of cancer biology and to developing novel therapeutic strategies. The Proteomics Shared Resource (PROTSR) at the Mayo Clinic Comprehensive Cancer Center (MCCCC) provides powerful proteomics tools to study a wide range of biomedical questions in cancer. These include biomarker discovery, signaling pathway analysis, and interactome analysis to targeted quantitation of proteins in clinical samples and development of diagnostic assays. With strong support from the Mayo Clinic leadership, Akhilesh Pandey (NTTM, MCR), a pioneer in mass spectrometry and proteomics, was recruited from Johns Hopkins University to Mayo Clinic in 2018. He became the new PROTSR Director in 2020, leading its transformation from offering routine protein characterization services to developing and deploying cutting-edge and novel proteomics techniques for accelerated discoveries by MCCCC investigators. PROTSR proposes three Specific Aims: Aim 1: Provide MCCCC members with key services in protein analysis, proteomics, and mass spectrometry to enhance cancer research activities. Aim 2: Provide MCCCC members with consultation on project planning, experimental design, and data analysis and interpretation, as well as convenient in-house access to all of its services. Aim 3: Evaluate and implement advanced instrumentation and novel technologies to enhance current services and to support the implementation of new service lines. The PROTSR, composed of 14 faculty and staff, offers nine service lines. Most proteomics services are performed using various mass spectrometry-based LC/MS-MS systems. These include gel-band ID, label-free quantitative proteomics using data-dependent or data-independent acquisition and tandem mass tag-based quantitative proteomics. Additional services include the analysis of post-translational modifications, including global phosphoproteomics and analysis of antibody enrichment–based acetylome, ubiquitylome, methylome, and tyrosine phosphoproteome. Recently, three new service lines have been introduced: targeted analysis using multiple reaction monitoring, single-cell proteomics, and spatial proteomics via laser capture microdissection. In addition, the PROTSR offers proteomics services on non-MS platforms, including single-cell secretome and signaling analysis on the IsoSpark platform, the Olink HT Platform for measuring about 5,300 proteins using Proximity Extension Assay technology with next-generation sequencing (NGS) readouts and peptide synthesis and peptide microarrays. 40% of revenue in the current funding period has come from MCCCC members. Member Utilization 2019-2023: 108 Total (1 CPCS, 4 REDI, 26 CGSM, 30 CII, 26 NTTM, 21 ACTS) Publication by Members: 26, 8 with Impact Factor >10