Proteomics & Metabolomics Core

Duke University, Durham NC

Investigators

Linked publications, trials & patents

Abstract

The DCI Proteomics and Metabolomics Core Facility (DPM) provides the wide variety of mass spectrometry- based untargeted (‘omic) and targeted qualitative and quantitative capabilities for proteomics and for targeted metabolomics which are needed to support basic science studies. The lab also has the scale needed for support of clinical research studies, including biomarker discovery and biomarker verification experiments. The DPM is equipped with seven high-resolution mass spectrometers, five triple-quadrupole mass spectrometers, and eleven Ultra Performance Liquid Chromatography (UPLC) systems. This equipment includes state-of-the-art mass spectrometers including an Orbitrap Astral (Thermo), a Fusion Lumos Tribrid with Electron Transform Dissociation and UV Photodissociation (Thermo), an Exploris 480 (Thermo), Sciex 6500+ QTrap and Sciex 6500+ TQ. The DPM has a full-time staff of seven scientists, including three PhDs (two Research Professors, one scientific staff member). This group has over 120 years’ combined experience in mass spectrometry and more than 200 authored or co-authored publications (counting publications with DMP members as co-authors). The resource is located in a ~8,100 sq. ft. laboratory in the Chesterfield Building in downtown Durham, custom built for mass spectrometry-based proteomics and metabolomics. By working closely with vendors to obtain extensive discounts, prudent use of DPM Betterments Funds towards the new equipment, and the DCI CCSG support, the DPM has maintained cost-effective (revenue neutral) support for the DCI at state- of-the-art levels. The DPM’s objective is to generate high-quality data by providing full service to its customers. This includes initial consultations to create optimal experimental designs, use of rigorous QC protocols and standards from sample preparation through sample analyses, and generation of detailed reports to ensure clarity on experimental approach and results. Use of a Laboratory Information Management System (LIMS) ensures sample integrity (unique Project Numbers and Sample IS numbers automatically assigned by the LIMS), and the use of a timestamped DukeBox data repository ensures data integrity. In FY22, the DPM provided services to 38 DCI members, who accounted for 32% of all users and represented 6 DCI Research Programs. Use of this shared resource by DCI Members contributed to >15 publications over the project period demonstrating the value of services offered by the resource. During this time, the DPM received support from the DCI CCSG and Institutional Support from the SoM in the form of new service lines (single cell proteomics initiative) and new instrumentation (Opentrons OT-2 and Thermo NeoVanquish UPLC for low-input proteomics).