Montana State University

Department of Chemistry and Biochemistry

Facilities/Instrumentation


The New Chemistry Building
Chemistry and Biochemistry Building

     The Department of Chemistry and Biochemistry at Montana State University understands the important roll of instrumentation in research and training. Our department is committed to providing students, faculty, and staff with the instruments they require to stay at the forefront of research.

     Structural Biology is well represented in our department and both NMR and X-ray equipment are available. Chemists and Biochemists alike benefit from the excellent NMR Instrumentation; 600, 500, 300, and 250 MHz NMR spectrometers. These instruments are used in routine analysis of small molecules and also protein structural determination.

     The center for X-ray crystallography has a macromolecular X-ray program.

     Computational chemistry is being served by a 64 processor Linux cluster with Intel 32-bit and 64-bit processors organized into 14 nodes. These nodes are equipped with the latest versions of a broad spectrum of molecular modeling and electronic structure calculation software, such as Gaussian, Jaguar, Amsterdam Density Functional, MOPAC2000, MacroModel, and Tinker. Intel and Portland Group compilers are available for software development.

     The Department also boasts high frequency CW and pulsed EPR instrumentation, a dynamic light scattering instrument, an isothermal titration microcalorimeter, an ultrafast femtosecond laser system, 3 tunable high resolution Nd: YAG pumped pulsed dye laser systems, and a quartz crystal microbalance capable of monitoring dissipation. Investigations of high energy gas-phase and gas-surface molecular interaction are conducted using a molecular beam apparatus that was originally designed by Nobel Laureate, Y. T. Lee, for crossed-beam studies of elementary reaction dynamics, and is one of the premier machines in the world for this purpose. Employing a pulsed hyperthermal atomic-oxygen beam, produced by laser detonation of O2, a wide range of high energy reaction are conducted with this apparatus. We have spectrometers for Raman, FTIR, fluorescence, CD/MCD, and X-ray photoelectron spectrometry. In addition the equipment housed in our department, campus microscopy capabilities include transmission electron microscopy (TEM), scanning electron microscopy with cryogenics (SEM), atomic force microscopy (AFM), confocal imaging, and laser micro dissection and capture.

     The mission of the Mass Spectrometry, Proteomics, and Metabolomics Facility is to seed methods, technology, and applications to research labs at Montana State University and affiliated programs. This facility offers a full range of services from single samples to complete shotgun proteomics and metabolomics projects.

     Periodic hands-on training sessions are offered by the Facility. The goal of the training modules is to expand facility access to researchers with little previous training in proteomics, metabolomics, or mass spectrometry. Individual training can also be arranged. Please contact the facility personnel listed below if you wish to be trained. The Mass Spectrometry and Proteomics Facility is supported with funding from the CoBRE Center for the Analysis of Cellular Mechanisms and Systems Biology and the Murdock Charitable Trust.

Instrumentation
      The mass spectrometry facility operates a variety of mass spectrometry instrumentation, each with advantages for specific types of analyses. If you have a specific project in mind, contact us to discuss possible options. The following list highlights some of the instrumentation and example applications. Of course, we are always interested in new applications, so contact us with specialized requests.

Agilent 6340 XCT Ion Trap with 1100 nano-HPLC
     The mass spectrometry facility operates two identical ion traps for proteomics studies. These systems are equipped with the Chip Cube source, which provides nanospray performance in a convenient platform: the enrichment column, selection valve, tubing, analytical column, and emitter are all packaged into a removable microfluidics chip. This permits every user to have their own dedicated, portable chromatography setup, reducing problems with carryover and downtime common to open-access facilities. The 6340 instruments are equipped with electron-transfer-dissociation fragmentation (ETD), providing MS/MS data for peptides with delicate post-translational modifications.

Bruker micrOTOF with Agilent 1100 HPLC
     The micrOTOF is an electrospray ionization (ESI) instrument with a time-of-flight (TOF) detector. The ESI source is a "gentle" ionization method, which makes it possible to analyze extremely large molecules such as proteins. The TOF mass analyzer gives high mass accuracy (~3ppm) and resolution (10,000) for confirmation of molecular formula and accurate protein/peptide fragment assignment. The Agilent 1100 HPLC delivers solvent flow rates between 10 microliters and 1000 microliters per minute, appropriate for typical analytical HPLC analyses. The micrOTOF is regularly used for evaluating recombinant proteins, providing accurate mass for novel organic synthesis products, quantitation of known metabolites, and for biophysical studies such as hydrogen-deuterium exchange of proteins.

Agilent 6520 Q-TOF with Agilent 1290 uHPLC
     Like the micrOTOF, the 6520 QTOF has an ESI source and TOF analyzer, but it has expanded functionality from several unique features. The QTOF is capable of MS/MS fragmentation, which is invaluable for determining the identification of unknown compounds. The 6520 also has improved resolution compared to the micrOTOF, and is equipped with a uHPLC for rapid high-performance chromatography. These two features make it ideal for quantitative analysis of metabolite extracts, which is further supported by the MassHunter and MassProfilerPro software packages. The 6520 is also Chip Cube compatible, permitting easy nano-HPLC.

Agilent 6538 Q-TOF with Agilent 1290 uHPLC
     The 6538 QTOF is an ultrahigh resolution mass analyzer that can be operated in high-resolution or high dynamic range modes. When interface with the 1290 ultrahigh pressure HPLC this system is ideal for quantitative analysis of complex metabolite extracts. Metabolomics data analysis is supported by XCMS, metaXCMS, MassHunter and MassProfilerPro software packages and the METLIN database.

Bruker maXis with Dionex 3000 nano-uHPLC
     For applications which require additional performance or features beyond the XCTs or micrOTOF, the maXs offers extremely high mass accuracy, resolution, sensitivity, dynamic range, and speed. By using a TOF mass analyzer, the maXis shares the rapid-chromatography capabilities of the 6520, but adds improved resolution, the ETD fragmentation option, and the sensitivity-enhancing ion funnel optics. The maXis is also equipped with a nanospray source coupled to a dedicated splitterless Dionex nano-HPLC.

Bruker Autoflex
     MALDI analyses are currently conducted on a Bruker Autoflex. This instrument is extremely functional for applications ranging from peptide identification to large polymer analysis. The Autoflex has MS/MS capabilities and can be used in an automated mode to collect MS and MS/MS data. In addition, the Bruker imaging software program is available for analysis of tissue, environmental, and fabricated samples. MALDI-TOF instruments provide an extremely low entry barrier for new users and are ideally suited for high-throughput screening.

GC-MS Agilent and Shimadzu instruments
     For GC analyses, we have two systems. An Agilent GCMS 5975 XL EI/CI MSD/DS and a Shimadzu QP-2010 GC with quadrapole mass analyzer. Both instruments have NIST compound libraries for identification of unknown molecules. The Agilent GCMS system also has MassHunter Data Analysis for GCMS and the new Fiehn GC/MS Metabolomics RTL Library.

2D Gel DIGE and Image Analysis Equipment
     The Facility possesses a full range of gel electrophoresis equipment including two DALT 2, 24cm gel tanks with capacity for 12 gels and a 24cm, six gel tank. Scanners include the GE Typhoon Trio (TM) variable mode scanner / imager with advanced spot evaluation software and a state of the art hyper-spectral imager for full wavelength data collection on a pixel by pixel basis.