Laboratory
The Mass Spectrometry Facility occupies 3050 sq. ft. of laboratory and office space on the second floor of the Biotechnology Center at the University of Wisconsin-Madison. This space is divided into three main rooms, each housing a combination of instruments, bench space, and workstations. There are a total of 88 linear feet of bench space for sample preparation and wet chemical work, as well as three fume hoods. The Core Facility shares use of a walk-in (208 sq. ft.) 4°C cold room and walk-in (72 sq. ft.) -20°C freezer and a dedicated -80°C freezer. A portion of the lab space has been tasked as a computer and meeting room, with several individual workstations, seating for clients and staff, and a printer. In addition to the laboratory space allocated on the second floor of the Biotechnology Center, the Mass Spectrometry Core Facility has part ownership of an additional mass spectrometer housed in a research laboratory on the 5th floor of the adjacent Genetics building, with 170 sq. ft. of lab space reserved for this instrument.
Clinical:
N/A
Animal:
N/A
Computer:
All mass spectrometers (see Equipment page) are connected to acquisition/processing computers running vendor software. There are 3 dual-monitor workstations located in our computer room for execution of processing and data analysis software. The Core Facility is connected via internal building network to two additional dedicated processing servers. The first of these contains dual Intel Xeon E5 2620 4-core CPUs @ 2.4GHz with 64GB RAM and running Windows Server 2012 R2. The second server contains dual Intel Xeon 4215 8-core CPUs @ 2.5GHz with 64GB RAM and runs Windows Server 2019. All processing workstations are running Windows 10 OS and are updated at least once a week. Two additional processing computers are located in lab space near the mass spectrometers. These computers are dedicated to analysis of lipidomic data and have specialized software installed for this purpose. These computers are Hewlett-Packard (HP) Z4 workstations, each of which incorporates an Intel Xeon W-2123 4-core CPU @ 3.6GHz with 16GB RAM running Windows 10. Some of the acquisition computers connected to mass spectrometers are required to run Windows XP OS due to limitations of the acquisition software. These instruments are on a segmented network to prevent vulnerability due to the age of the OS.
Office:
114 sq. ft. office space located immediately adjacent to the Core Facility used exclusively by the Director.
Other:
The Biotechnology Center houses several University core facilities, including the Gene Editing and Animal Model facility, Next-Gen DNA Sequencing facilities, Gene Expression facility and Bioinformatics Resource Center. By housing these facilities within a single building, and on adjacent floors, University researchers can easily access all of the necessary services to advance their research. Additionally, close contact between directors and staff of these facilities promotes discussions and allows for better guidance for principal investigators and students seeking advice on experimental design and analytical methods.
Equipment:
The following mass spectrometers are currently housed in the Mass Spectrometry Core Facility:
Agilent 6546 QTOF mass spectrometer connected to Agilent 1290 Infinity II UHPLC system. There are currently two of these instruments installed in the Core Facility, configured identically. The 1290 Infinity II UHPLC system consists of a high speed binary pump capable of pressures up to 1300bar (~18,000psi), a temperature-controlled multisampler, a temperature-controlled column compartment, and a isocratic pump. Both of these instruments are dedicated to lipidomics analysis, supporting diabetes research and other research efforts on campus.
ThermoFisher Scientific Orbitrap Fusion Lumos mass spectrometer coupled to a ThermoFisher UltiMate 3000 RSLCNano binary UHPLC with temperature-controlled autosampler. This instrument is connected to a dedicated acquisition and processing computer that controls both the mass spectrometer and the HPLC. This instrument is equipped with the electron transfer dissociation (ETD) fragmentation option for enhanced ability to sequence peptides containing labile modifications such as phosphorylation and glycosylation. The Mass Spectrometry Core Facility has part ownership of this instrument and shares acquisition time with Biochemistry Department Professor Dr. Michael Sussman.
ThermoFisher Scientific Orbitrap Elite mass spectrometer connected to an Agilent 1100 Nano flow HPLC system with temperature-controlled autosampler and temperature-controlled column compartment. This instrument is used for both proteomics and small molecule/metabolite analysis. When used for proteomic work, the instrument is configured for nano-flow HPLC, with flow rates at 300nL/min and separations achieved using ThermoFisher EasySpray 75µm i.d. columns coupled to a ThermoFisher EasySpray source. When used for small molecule or metabolomics analyses, the HPLC system is configured for analytical flow rates (200-500µL/min) into 2.1mm i.d. columns in the column compartment and using the ThermoFisher IonMax electrospray source. The mass spectrometer and HPLC system are connected to dedicated acquisition and processing computers.
Sciex 5500 QTRAP triple quadrupole/ion trap mass spectrometer connected to an Agilent 1100 Nano flow HPLC system with temperature controlled autosampler. This instrument can be configured with either TurboV ion source for analytical flow rates, or Nanospray III source for nanoscale flow rates. This instrument is connected to in-house pressurized air and a nitrogen generator for gas supplies. The mass spectrometer and HPLC system are connected to a dedicated acquisition and processing computer.
Sciex 3200 QTRAP triple quadrupole/ion trap mass spectrometer connected to an Agilent 1100 binary HPLC system with temperature-controlled autosampler and column compartment. This instrument is connected to in-house pressurized air and a nitrogen generator for gas supplies. The mass spectrometer and HPLC system are connected to a dedicated acquisition and processing computer.
ThermoFisher Scientific TSQ Quantum Discovery Max triple quadrupole mass spectrometer connected to an Agilent 1100 binary HPLC with temperature-controlled autosampler and column compartment. Nitrogen is supplied to this instrument via in-house air supply coupled to a nitrogen generator. The mass spectrometer and HPLC system are connected to dedicated acquisition and processing computers as described above.
Sciex 4800 MALDI TOF/TOF. The mass spectrometer is connected to a dedicated acquisition and processing computer as described above.
Agilent GC/MS 7890B/5977A system with an Agilent 7693 autosampler. The instrument is controlled by an acquisition and processing computer and includes the NIST spectral database for identification of unknowns and validation of known compounds.
In addition to the above mass spectrometers, the Core Facility possesses a number of additional pieces of equipment to enable our services and enhance analytical capabilities. These include:
Waters Alliance HT HPLC system comprised of a 2795 separation module, 2996 photodiode array detector and a Gilson fraction collector. This instrument is used for “offline” fractionation, which allows the use of solvent systems incompatible with mass spectrometry. This system connected to a dedicated acquisition and processing computer.
Agilent 1200 Series semi-UHPLC including a binary pump capable of pressures up to 600bar (~8600psi), degasser, and temperature-controlled autosampler and column compartment. This instrument is located on a cart for portability, which enables use of higher pressure UHPLC columns for enhanced separations with any mass spectrometer.
Savant SpeedVac centrifugal concentrator and vapor trap. The Core Facility possesses two of these systems for higher throughput.
Mettler AE50 and AE100 analytical balances, as well as a high-precision Mettler XSR205 balance.
Beckman Coulter Allegra 25R temperature-controlled centrifuge with rotors for plates, vials, and bottles.
Qiagen TissueLyser II bead-beating instrument for tissue homogenization and extraction.
Sutter P-2000 laser puller for in-house preparation of nano-scale HPLC columns and electrospray tips from fused silica capillary.
Cary 300 Bio UV-Visible spectrophotometer. This instrument has an independent data system and external temperature controller.
Powerex WhisperAir oil-less scroll pump. This air compressor is coupled to a large external tank and provides compressed air to both a nitrogen generator and an air drier which in turn supply these gases to multiple mass spectrometers.
Millipore Milli-Q Reference water system. This provides >18MΩ/cm resitivity water for various buffer and solvent needs in the Core Facility.
The Core Facility also possesses several benchtop centrifuges, heating blocks, water baths, vortexers, and stirring plates, as well as a pH meter, a 24-position manifold for parallel solid-phase extractions, and a 27-sample manifold for drying samples under nitrogen with heating.