University of Illinois
The University of Illinois Urbana-Champaign (UIUC) 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, available to local researchers.
Instruments
The UIUC Cellular Mass Spectrometry Facility, run by NIDA PI Sweedler, has multiple mass spectrometry resources that are available to the Center. These include the following Bruker instruments (as part of our being a Bruker Center of Excellence): ultrafleXtreme MALDI-TOF/TOF (installed March 2023), solariX XR ESI/MALDI FT (7 Tesla), timsTOF Pro LC-MS System, and EVOQ Elite triple quadrupole, a Bruker timsTOF flex MALDI-2 instrument (installed Fall 2023), and a timsMetabo (intalled Spring 2026). The facility also has an Agilent 6495C Triple Quadrupole (installed Summer 2023).
Additional analytical instruments expand our services and applications. The facility has a range of separation and sampling systems. We have interchangeable front-end separation options that include a 908 Devices ZipChip (an automated capillary electrophoresis system), a Newomics multiemitter UniESI source for custom CE applications, a Thermo UltiMate 3000 x2 Dual microbore HPLC/UHPLC system with automatic column switching for quantitation and structural characterization of small molecules, as well as several laboratory-constructed single-cell capillary electrophoresis systems. The Bruker triple quadrupole instrument is hyphenated to a Bruker Advance UHPLC with a CTC Autosampler and OLE module for metabolite quantitation, and a Agilent 7100 CE (new in 2024) is interfaced to the Agilent 6495C Triple Quadrupole mass spectrometer. Our sampling experiments are supported by two micropipette pullers, dissection equipment, a vibratome, an AutoMate Scientific BSC-1 brain slice chamber, and others. We have tissue culture hoods, cell incubators, and all necessary equipment for primary cell culture and preparing high quality MSI samples. This includes a Shimadzu Chip1000 Chemical Printer for precise matrix and solution applications to MALDI targets or slides, an HTX M5 Sprayer, and an HTX Sublimator (installed May 2024) for automated coating of the MALDI targets. The group has a SCIEX capillary electrophoresis system (800 Plus Pharmaceutical Analysis System) with interchangeable UV, photodiode array, and laser-induced fluorescence detectors with zeptomole detection limits for metabolites (such as chiral metabolites) that are difficult to differentiate via CE- and LC-MS.
Available software packages include PEAKS Studio, Mascot, MarkerView, MATLAB Bioinformatics Tool-Box for statistical analysis of raw mass spectrometry data, and a complete suite of Bruker software solutions (e.g., SCiLS Pro/Premium, MetaboScape, MS-MetaboBase, ClinProTools, and more).
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, the Institute for Genomic Biology Biocluster, and various other high-performance computers available at the National Center for Supercomputing Applications.
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 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.