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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 [email protected] to discuss how we can support your research.

IDeA Facility Equipment

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.

Targeted Proteomics: Quantify levels of a small set of target proteins in a large number of samples.

Bioinformatics: Analysis and interpretation of complex proteomics data to inform a biological question.