Overview of Equipment and Services

The IDeA National Resource for Quantitative Proteomics provides a full range of services for protein characterization by mass spectrometry, including protein identification, mapping of post-translational modifications, global proteomics, and quantitative comparison of proteins in biological samples using state-of-the-art equipment. Our 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 sample. Comprehensive data analysis is also included with all services. We are committed to working with each investigator to adapt our approach to fit specific research goals and to providing results in customized publication-quality form. Please contact us at IDeAproteomics@uams.edu to discuss how we can support your research.

IDeA Facility Equipment:

Orbitrap Tribrid Mass Spectrometers

The Thermo Orbitrap Eclipse Tribrid system (Thermo Scientific) is the latest generation of the state-of-the-art Orbitrap mass spectrometry technology. The facility 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 quadrupole mass filter allows precursor ion selection, enabling parallel use of the mass analyzers and synchronous precursor selection for MS3 analysis. An ion-routing multipole serves as a higher-energy collisional dissociation (HCD) cell and also transfers ions efficiently between the Orbitrap and linear ion trap mass analyzers, allowing use of either mass analyzer in combination with any ion fragmentation technique. The ultra-high-field Orbitrap mass analyzer has a resolving power of up to 500,000 FWHM and 45 Hz scan rate. A linear ion trap performs collision-induced dissociation (CID) and electron-transfer dissociation (ETD).

Orbitrap Exploris 480 Mass Spectrometer

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 over earlier generation instruments in this class include significantly enhanced instrument sensitivity largely 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 facility is equipped with two of these instruments, which are used primarily for data-independent acquisition (DIA).

TSQ Quantiva Mass Spectrometer

The TSQ Quantiva (Thermo Scientific) is a triple quadrupole instrument used exclusively for selected reaction monitoring (SRM) experiments for targeted quantitative proteomics. The advantage for SRM experiments on the TSQ Quantiva is rapid switching between transitions with a set dwell time. The result is that a large number of peptides can be measured in a single run with a consistent 1.5 cycle per second acquisition rate, which gives at least 20 data points for all chromatographic peaks. Scheduling is used for all experiments based on the known retention times of targeted peptides. SRM on a triple quadrupole mass spectrometer remains a workhorse experiment for quantitative analysis with outstanding precision, lower limits of detection, and robust instrument operation.

Q Exactive Plus Mass Spectrometer

The Q Exactive Plus (Thermo Scientific) is a hybrid quadrupole-orbitrap instrument used for parallel reaction monitoring (PRM) in our targeted quantitative proteomics services. Orbitrap instruments are known for high m/z resolution, with values ranging from 17,500 to 280,000 on the Q Exactive Plus. The advantage for PRM experiments on the Q Exactive Plus is the high-resolution product ion m/z scan and the increased specificity of detection this m/z resolution provides via smaller m/z tolerances in the data analysis.

UltiMate 3000 Binary Analytical Liquid Chromatography System

The UltiMate 3000 UHPLC system (Thermo Scientific) is capable of precise and efficient offline fractionation of complex protein digests. This system is used in the facility workflow to fractionate peptides at basic pH in order to complement the acidic pH separation performed during liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) analysis. The UltiMate 3000 can sustain pressures as high as 9000 psi and flow rates as low as 50 nL/min. The system includes an analytical autosampler and fraction collector to allow efficient processing of large numbers of samples, as well as a UV detector to monitor peptide elution and prevent cross-contamination.

Computing Resources

High Performance Computing (HPC) Cluster: Our HPC is composed of 96 traditional Xeon CPU nodes each with 28 cores and 128 GB of memory (2688 CPU cores), 96 Xeon Phi nodes each with 64 cores (80 with 384 GB of memory and 16 with 192 GB of memory; 6144 Phi cores total), 4 Xeon nodes with 24 cores and 128 GB of memory plus 2 NVIDIA GPUs (96 CPU cores, 8 GPUs with 27,264 total cores), 6 management/login/storage interface nodes, and 1.9 PB of high speed storage (DDN Gridscaler). All components are interconnected via 100Gbps Omnipath interconnects and attached to external storage and the Internet (both commercial and I2) with redundant 10 Gbps Ethernet interfaces. Intermediate storage is provided by a 350 TB NAS and long term/backup storage is provided by a 4.2 PB object storage system (Dell/EMC ECS appliances).

PowerStation GX2: We have two PowerStation GX2 Advanced Workstations (PSSC Labs). Each Linux workstation contains 40 Intel Xeon Scalable Processor Cores for a total of 80 cores with hyperthreading enabled, two GOLD 6148 processors, 128 GB of high performance memory, 22 TB of RAID5 storage, CentOS 64-bit operating system, and a maintenance kit from PSSC Labs.

Dell Windows PCs: The facility maintains ten Dell Precision workstations, each with solid state hard drives and 128 GB RAM, supporting a full range of data analysis software, including an in-house Mascot Server (Matrix Science), several MaxQuant (Max Planck Institute) installations, Scaffold Q+S and Scaffold DIA (Proteome Software), and PEAKS Studio (Bioinformatics Solutions).

Services Provided:

• Discovery proteomics: large-scale identification and quantification of proteins or protein posttranslational modifications from a complex biological sample. More information on the Discovery Proteomics Service Line can be found here.
• Targeted proteomics: quantify levels of a small set of target proteins in a large number of samples. More information on the Targeted Proteomics Service Line can be found here.
• Bioinformatics: analysis and interpretation of complex proteomics data to inform a biological question. More information on the Bioinformatics Service Line can be found here.