Contact
Please contact Ricky Edmondson, Ph.D., Co-Director, at rdedmundson @uams.edu or Samuel Mackintosh, Ph.D., Co-Director, at mackintoshsamuelg@uams.edu to discuss how we can support your research.
Personnel
Edmondson is a Professor of Biochemistry and Molecular Biology and Co-Director of the Shared Resource. He has over 20 years of experience in proteomics research and served as Co-Director since 2006.
Mackintosh is a Professor in the Department of Biochemistry and Molecular Biology and Co- Director of the Proteomics Shared Resource. He has worked in the Proteomics Shared Resource since 2006.
- Other Personnel – Five staff members, two bioinformaticians, and two administrators.
Major Services
The Winthrop P. Rockefeller Cancer Institute Proteomics Shared Resource provides a full range of services for biomarker discovery and protein characterization by mass spectrometry, including protein identification and post-translational modification mapping, global proteomics, and quantitative comparison of proteins in biological samples using state-of-the-art equipment. The services are comprehensive, including complete sample preparation starting from cultured cells, frozen or FFPE tissue samples, serum or plasma, IP, and other affinity purifications as well as many other types of biological samples. Additionally, the Proteomics Shared Resource provides full bioinformatics support to the point of publication or grant submission of proteomics data for Winthrop P. Rockefeller Cancer Institute members.
Technologies and Equipment
- Orbitrap Astral Mass Spectrometer – The Thermo Orbitrap Astral Mass Spectrometer system (Thermo Scientific) features significant advancements over previous generation Orbitrap instruments in sensitivity and acquisition speed. The key feature of this instrument is the Astral Mass analyzer that has a 30-meter asymmetric time-of-flight path capable of resolution up to 80,000 FWHM downstream of a 200 Hz ion processor and an ion foil that tightly focuses the ion beam with minimal transmission loss. In combination with an ultra-high-field Orbitrap mass analyzer, the hybrid instrument can achieve greater depth with less sample in shorter acquisition times than previously possible. The Orbitrap Astral is used primarily for data-independent acquisition (DIA) quantitative proteomics.
- Orbitrap Tribrid Mass Spectrometers – The Thermo Orbitrap Eclipse Tribrid system (Thermo Scientific) is a state-of-the-art Orbitrap Mass Spectrometer technology. The resource operates two Eclipse systems as well as two Orbitrap Fusion Tribrid instruments. The Orbitrap Tribrid systems combine a quadrupole mass filter with Orbitrap and linear ion trap mass analyzers in a novel configuration that maximizes ion transfer efficiency, allowing flexible combinations of different fragmentation techniques, scanning modes, and mass analyzers. The Eclipse systems are used for tandem mass tag (TMT) quantitative proteomics, while the Fusion systems are used for data-dependent acquisition quantitative proteomics.
- Orbitrap Exploris 480 Mass Spectrometers – The Orbitrap Exploris 480 mass spectrometer (Thermo Scientific) combines a quadrupole mass filter with a high-field Orbitrap mass analyzer and high-capacity ion transfer capability to optimize scan rate, sensitivity, and resolution. Improvements to earlier generation instruments in this class include significantly enhanced instrument sensitivity due to improved ion transfer capabilities, improved instrument robustness and serviceability, and compatibility with next-generation ion sources, such as the FAIMS Pro (high-field asymmetric ion mobility spectrometry) ion source. The resource is equipped with two of these instruments, which are used primarily for DIA proteomics.
- Sample Preparation and Storage – The resource has the equipment necessary to prepare and store protein samples for mass spectrometric analysis, including an UltiMate 3000 LC system (Thermo Scientific), Opentrons OT-2 automated liquid handling system, Tecan Resolvex A200 automated positive pressure workstation, sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) apparatus, power supplies, incubators, microcentrifuges, sonicators, speedvac, and −20°C and −80°C freezers.
- Computer Equipment – All personnel have networked personal desktop computers or laptops linked to a docking station and are networked to multiple printers, including a high through-put multifunction device, which provides printing, faxing, and scanning capabilities. Likewise, the Proteomics Shared Resource has priority access to a computer cluster housed in the UAMS Biomedical Informatics Department as well as full access to a PowerStation GX2, which contains 16 2.0GHz E5-2600 Cloud Ready processor cores, 64GB of memory, 8TB of RAID5 storage, and CentOS 64-bit operating system. The Shared Resource has remote access to Argon (the University of Arkansas at Little Rock’s Rocks 5.4 cluster), which is built for running large-scale distributed-memory multiprocessing with message passing interface as well as for running large numbers of independent jobs. The Shared Resource also has remote access to a shared memory machine by HP (Erbium) and is equipped with a number of applications (MATLAB, Maple, R, Bowtie, Tophat, Cufflinks, fastX-toolkit, High-Performance Linpack [HPL], Octave, Gaussian G03 and G09, VASP, COMSOL, FDTD, Hadoop) and useful libraries. The Shared Resource also has oversight of 200TB of NAS data storage. The storage system was purchased through Dell, and the rack is housed in the IT department.