Montana State University

Center for the Analysis of
Cellular Mechanisms and
Systems Biology

Montana State University
Department of Chemistry and Biochemistry
Chemistry and Biochemistry Building
P.O. Box 173400
Bozeman, MT 59717


Professor Edward A. Dratz

Fiscal/Program Manager

Renee Sabo

For more information

Tel: (406) 994-7128
Fax: (406) 994-5407

CoBRE at Montana State University

ChemBiochem EPS Cooley Roberts

The Center for the Analysis of Cellular Mechanisms and Systems Biology

CoBRE Center Overview

The CoBRE Center for the Analysis of Cellular Mechanisms and Systems Biology at Montana State Univeristy is working to build and strengthen systems biology at MSU.  In support of these efforts, we have established a Proteomics, Metabolomics, Mass Spectrometry and NMR Facility with leading edge capabilities. The purpose of this core is to provide access to state-of-the-art equipment and training of personnel in advanced analytical techniques in support of COBRE research and the greater Montana research community. The facility is built on the concept that well trained users can conduct proteomics and systems biology-related research at a level higher ad at lower costs than provided by a service lab. The Facility is located in the new Chemistry and Biochemistry Building on the MSU campus.

Facility Equipment

The foundation of the facility is a fleet of 9 mass spectrometers and a 600MHz NMR with cyro prob autosampler.  Instrument acquisition has focused on platform diversity and usefulness. Proteomics work is supported by a Bruker Maxis Impact Ultra High Resolute Resolution QTOF interfaced with a Dionex 3000 nanoflow LC for shotgun analysis, a Bruker Amgon EDT High Resolution Ion trap and a 6520 QTOF high resolution mass spectrometer, and a Bruker Autoflex III MALDI-TOF/TOF (with imaging capability).   Together these instruments allow experiments ranging from single protein identifications to large scale shotgun proteomics projects to be conducted.  Software in support of proteomics includes; MASCOT, Phenyx, and Spectrum Mill for protein identification and ProteinScape and Mass Hunter/Mass Profiler for data analysis and processing. 2D gel work is supported by BioRad and GE gel systems with capacity for 48 24cm gels. In addition, the facility has a Typhoon high resolution fluorescent scanner, Resonon Hyperspectral 2D Fluorescent Gel Scanner, Progenesis SameSpots 2D DIGE software (Nonlinear Dynamics Ltd), and hepa-filtered laminar flow hood.  Metabolomics and small molecule analysis is supported with an Agilent 6538 ultra high resolution QTOF interfaced with an Agilent 1290 ultrahigh pressure LC and 2 GCMS instruments.  Metabolomics capabilities are also available using NMR analysis, with automated sample changer .  Data analysis tools for metabolomics include XCMS, metaXCMS, Mass Hunter, Mass Profiler Professional, and Chenomx NMR Suite as well as the. NIST and METLIN databases.

The facility can typically return data within 24 hrs for routine samples. In an attempt to improve performance and usability, the Chemistry and Biochemistry facility is part of a larger effort to centralize the Core facilities at MSU (not physically) so that access to leading edge instrumentation will continue for years to come [see  and] A new online scheduler is now in operation and all instrument reservations should be made using this scheduler. Please contact Jonathan Hilmer about access to the scheduler site.

The facility expansion has been driven by three significant funding awards.  First, the COBRE Center for Cellular Network Analysis lead by PI Dr. Dratz.  Second, a Murdock instrumentation grant developed by Drs. Dratz and Bothner.  Third, a supplement for the establishment of NMR and mass spectrometry-based metabolomics and translational opportunities with the University of Washington, lead by Drs. Copie and Dratz.  A common theme in each of these proposals was an emphasis on education and training of users.  We take the training seriously and believe that skilled users will be able to realize new applications of mass spectrometry that will allow them to advance their research and careers.

If you have questions about capabilities, training, or general comments, please send them to either Jonathan Hilmer (Facility Manager), or Brian Bothner (Director)

Instrument Highlights:

Bruker MaXis Impact, the blue giant in the back corner, has ultra high resolution and accuracy in the Q-TOF instrument class (< 1 ppm).  Nanospray HPLC and ESI source and has MS/MS capabilities for peptides and small proteins.  Use of this instrument is focused on shotgun proteomics and the investigation of protein post-translational modification. The Bruker ProteinScape software package, which facilitates integrated data analysis for comprehensive systems biology projects is available.

Agilent 6538  Agilent’s top-of the line Q-TOF.  This instrument is currently being used for small molecules work including metabolomics.  Agilent’s next generation UPLC (ultrahigh pressure) 1290 HPLC (with diode array detector) can be used to reduce the length  and increase the resolution of complex chromatography runs, and it has a full wavelength detector that can be utilized to follow sample absorbance spectra when needed.  Mass Hunter and Mass Profiler Professional software can be used to rapidly compare complex samples (with statistical analysis), search for molecules or fragmentation patterns of interest and search the METLIN database of compounds ( > 23,000 entries).

Bruker Autoflex III, MALDI-TOF-TOF instrument.  The Autoflex III can be used to analyze molecules across an extremely wide range of molecular weights.  In addition, ions can be selected for fragmentation, making this system very attractive for rapid identification of peptides and proteins along with many other molecules such as lipids, carbohydrates, and nucleic acids.  An added feature is the ability to create an image of a sample based on the molecular composition.  This can be used to study biofilms, tissue sections, surface treatments, and more. We are also happy to announce that our proteomics support now includes running of 2D gels and DIGE analysis.  Full metabolite profiling, molecular formula generation and statistical analysis for simple and complex samples is available as well.