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University of Illinois

The University of Illinois at Urbana-Champaign has one of the leading Chemistry Departments in the world, as well as two interdisciplinary research institutes--the Institute for Genomic Biology (IGB) and the Beckman Institute for Advanced Science and Technology (BI)--having expertise in bioengineering and neuroscience. The facilities in these units offer strong support for Center research, with these multidisciplinary programs enabling many aspects of the Center’s mission. In addition, the University of Illinois is home to the National Center for Supercomputing Applications and Blue Waters supercomputer infrastructure, which are made available to local researchers.

Instruments

The Sweedler group, with laboratory space in both Roger Adams Laboratory (RAL) and the BI, has multiple mass spectrometry resources that are available to the Center. The group has its own Bruker ultrafleXtreme MALDI-TOF/TOF mass spectrometer and six electrospray instruments, including a Bruker maXis 4G tandem Qq-TOF mass spectrometer (80,000 resolution), a Bruker Impact HD Qq-TOF (50,000 resolution), a Bruker ion trap amaZon Speed ETD (20,000 resolution), a Bruker micrOTOF Benchtop ESI-TOF mass spectrometer (interfaced to a home-built capillary electrophoresis system), a Bruker EVOQ Elite triple quadrupole, a Bruker solariX XR ESI/MALDI FT (7 Tesla) high resolution mass spectrometer, and an ABI QSTAR with interchangeable ESI and MALDI sources that has also been adapted to work with a C60 ion source in SIMS mode. Four of the Bruker ESI instruments are tandem mass spectrometers for structural characterization and/or quantitation of small molecules, peptides, and proteins, and have CaptiveSpray nanoBooster ion sources available as interchangeable options. The Bruker micrOTOF is hyphenated to a laboratory-built interface for small volume and single cell CE sampling and separation. The Bruker Maxis 4G has interchangeable front end separation options that include another laboratory-built CE system and a Thermo UltiMate® 3000 x2 Dual microbore HPLC/UHPLC system with automatic column switching for quantitation and structural characterization of small molecules. The triple quadrupole instrument is hyphenated to a Bruker Advance UHPLC with a CTC Autosampler and OLE module for metabolite quantitation. The Bruker Impact HD and Amazon Speed ETD are equipped with a Thermo UltiMate® 3000 nano-  and capillary-scale LC, respectively, and both are used for high throughput peptide structural characterization.

Additional analytical instruments expand our services and applications. A stand-alone analytical scale Waters Breeze 2 HPLC system with PDA detector and fraction collector enables off-line 1st stage separation of crude biological samples in preparation for 2nd stage LC-MS or LC-MS/MS measurements. A Bruker PROTEINEERfc is a liquid handler able to deposit samples from the capillary-LC on well plates or Bruker MALDI targets for offline MS and MS/MS analysis using the Bruker ultrafleXtreme mass spectrometer. A Shimadzu Chip1000 Chemical Printer allows for precise matrix and solution applications to the MALDI targets for imaging purposes. The group also has three research-grade inverted microscopes (one each with differential interference contrast and fluorescence) and maintains three electrophysiology rigs capable of intracellular and extracellular recordings in voltage clamp, current clamp, and/or patch clamp modes. Rigs include air tables, stimulators, differential and high impedance amplifiers, digitizers, and micromanipulator systems. Electrophysiological experiments are supported by two micropipette pullers. Dissection equipment includes a vibratome, an AutoMate Scientific BSC-1 brain slice chamber, and two Leica cryostats. Two cell culture incubators and two certified biological safety cabinets with laminar flow are suitable for culturing mammalian neurons.  

Bioinformatic Resources

The Rodriguez-Zas lab houses a number of state-of-the-art high performance computer systems including multiple workstations, each powered by dual Xeon 3.3 GHz processors, 12TB disk space and 128GB memory, and multiple high performance PCs. There resources are located in three adjacent computer labs within a 5-minute walk from the Center’s Analytical Core. The Center labs at the University of Illinois campus benefit from high network connection speeds of 10 Gbps. These resources enable prompt management and analysis of Big Data proteomic, metabolomics and DNA and RNA Next Generation sequencing data using advanced models and computational intense methods. The workstations are used to develop and maintain the following public web-based systems: a) BEEHIVE, a suite of integrated tools to manage and analyze transcriptome experiments, b) NeuroPred, a prohormone processing and peptide predictor, and c) PepShop, an integrated suite of database resources and proteomic tools to facilitate the annotation and identification of peptides. Software resources in the Rodriguez-Zas lab include statistical packages (e.g., SAS and R), open-source software for peptide identification (e.g., OMSSA, X!Tandem and Crux), open-source software for next generation sequencing analysis (e.g., Bowtie, Tophat and Cufflinks), and various programming languages (e.g., Python, JAVA, Perl, and C/C++). Additional high-performance computer resources accessible to the lab include the University of Illinois Campus Cluster (a 52 core cluster), the Institute for Genomic Biology Biocluster (24 nodes with 192 processors), and various other  high performance computer available at the University of Illinois such as Blue Waters supercomputer infrastructure.

Other Resources

In addition to Sweedler group instruments, a shared 11 T FTMS located at the IGB, and a Thermo Velos Pro linear ion trap housed at the Roy J. Carver Biotechnology Center (CBC), are used as needed. Two secondary ion mass spectrometers are available in the Frederick Seitz Materials Research Laboratory. Center staff has direct access to one of these instruments and can run samples on the other under the supervision of the laboratory's staff, and the School of Chemistry has its own Mass Spectrometry Laboratory. The CBC provides peptide sequencing, peptide synthesis, and antibody production; this Center has an automated DIGE system and several mass spectrometers, and a professional staff with expertise in metabolomics and proteomics measurements that can be used on a fee for service basis. RNA-Seq transcriptome experiments will be done at the DNA services, High-Throughput Sequencing and Genotyping Unit of the CBC. The DNA Services unit prepares libraries and generates DNA templates and sequence data using, among others, two Illumina Genome Analyzer IIx and two HiSeq2000 to provide next-generation sequencing technologies (maintained and used by professional staff). Other School of Chemistry facilities available include a machine shop (manned by six full-time master machinists), a professional quality drafting shop, a three-person glass shop, and an electronics shop.


Northwestern University

The research enterprise at Northwestern University is distinguished by its ability to define and lead interdisciplinary research. From the University culture of cooperation and collaboration, as laid out in the University’s strategic plan, interdisciplinary research is identified as one of Northwestern’s hallmarks and a foundation upon which Northwestern will build its future.

Instruments

The Kelleher research group has access to many top of the line Fourier-transform (FT) mass spectrometers. These instruments are capable of high mass accuracy measurements of proteins and peptides. Four are 7 or 12 Tesla LTQ-FTs (Thermo Fisher). The 12 Tesla instruments were constructed in collaboration with Thermo Fisher engineers. The group also has access to six other mass spectrometers: a TSQ Quantum Ultra Triple Quadrupole, an Orbitrap Elite, two Q-Exactives, an Exactive, and a Waters Q-TOF Premier. They also have direct access to three Dionex and two Eksigent nano-LC systems in addition to a CTC autosampler and several Agilent chromatography systems for higher flow rates. In addition, they house two commercial and over 20 custom “standard” GELFrEE electrophoretic devices as well as five custom isoelectric focusing devices and five electrophoretic power supplies up to a 3 kV rating. They have a 1.5 HP mill/drill press to machine simple parts. Instruments are located in the basement and third floor of the Richard and Barbara Silverman Hall for Molecular Therapeutics and Diagnostics on the Evanston Campus of Northwestern University.

Bioinformatic Resources

Northwestern staff have access to a large network, including a 168 core computing cluster for top down proteomics data analysis and processing, as well as the new 3,000 Quest High Performance Computing Cluster at Northwestern University. The assets of this facility include: architecture: IBM; number of nodes: 375; number of Cores: 3000; processor: Intel Nehalem E5520, 64-bit, 8M Cache, 2.26 GHz, 5.86 GT/s Intel® QPI, 1066Mhz FSB; memory: per node (per Core) 48GB's (6GB's), Type: DDR3; interconnect: Infiniband; parallel file system: GPFS (120 TB's).

Other Resources

All other required support facilities are available at Northwestern, including electrical and machine shops.