Department of Chemistry

Mass Spectrometry Facility

The Mass Spectrometry Facility in the Chemistry Department provides support for the analysis of a wide range of molecules using mass spectrometry based techniques, including a suite of modern instrumentation.


The Mass Spectrometry facility is available to all faculty, post-doc researchers, graduate and undergraduate students. Most facility instruments are available in an open-access manner to trained users. For research projects that required extensive mass spectrometric analysis, please schedule time with our Mass Spectrometer Specialist to discuss specific mass spec needs, instrument capabilities, and receive training for the most effective use of the mass spec facility. Assistance will be provided with data interpretation, sample preparation, experimental designs, and methods development.

Mass Spectrometer Specialist

Submit Samples

Users may submit samples for mass analysis using the Mass Spectrometry Request Form or in GeoChem 408 for sample submission. 

Mass Spectrometry Request Form



The facility maintains two GC-MS, three LC-MS, MALDI-MS, and a standalone HPLC system.

The mass spectrometers offer electron impact (EI), electrospray (ESI), atmospheric chemical ionization (APCI), and matrix assisted laser desorption ionization (MALDI) ionization modes that cover a variety of analytes of interest. Available software resources include instrument control and data analysis programs Xcalibur, MassHunter, ChemStation, SpectrumMill, Bioworks/Sequest. Routine mass spectrometric measurements performed in the facility include HRMS molecular formula confirmation, structural elucidation by MSn tandem mass spectrometry, qualitative as well as quantitative analysis of small molecules: synthetic intermediates, natural products, metabolites, and organometallics.

For macromolecules, we offer mass analysis of synthetic polymers, peptides and purified intact recombinant proteins and synthetic oligonucleotides. 

The 5973N series GC/MSD system has a single quadrupole mass analyzer, 6890 GC and 7683 autosampler and 100 vials sample tray.  This system equipped with standard EI source, unit mass resolution, mass range 1.6 – 800 u, SIM (30 ion x 50 groups), split/splitless injection, GC/MSD is controlled by Agilent MSD ChemStation software. NIST 2008 EI spectra library is installed with the Chemstation for spectral confirmation. This instrument is used mainly for analysis of volatile organic compounds and synthetic reaction mixtures. Trained users select from a menu of standard methods to analyze their samples. The default capillary GC column on this instrument is 0.25 mm i.d., 30 m Agilent HP-5MS. Mass spec facility also offer HP-1, DB-/WAX, and chiral GC columns for different applications.

The 5977A series GC/MSD system has a single quadrupole mass analyzer, 7890B GC and 150 vials 7693 autosampler and sample tray. This GC-MS provide high level of performance and productivity with standard electron EI source, mass range 1.6 – 1050 u, synchronous SIM/scan operation, RTL ready that allow creation of permanent and universal methods, GC/MSD data acquisition and analysis with both MassHunter and ChemStation. This instrument has superior sensitivity, particularly for nature products and metabolites analysis.

Agilent 6230 time-of-flight LC-MS system couples accurate mass TOF with the 1260 Infinity II liquid chromatography, which is equipped with dual electrospray (ESI) ion source and Multiple Wavelength UV Detector (MWD). This TOF LC/MS achieves resolution up to 20,000 (FWHM) and sub 1-ppm mass accuracy. It is capable of screening, profiling and identification of small molecules, large biologic compounds, and everything in between.

Agilent 6530 is a quadrupole time-of-flight (Q-TOF) accurate mass LC-MS system, equipped with both ESI and APCI ionization sources.  The mass spectrometer is a high accuracy (< 2 ppm in the MS mode and < 5 ppm in the MS/MS mode with internal calibration), high resolution (20,000 FWHM mass resolving power).  Mass range m/z 50 – 3200 for high resolution mode and m/z 100 – 20,000 for extended mass range. The frond-end of this LC-MS system is Agilent 1260 Infinity Binary LC, with a flow range from 0.05 – 5 mL/min at pressure up to 600 bar suitable for narrow bore 2.1 mm ID HPLC columns, matching the requirements for LC-MS operation. The 1260 LC also consisted of a high performance autosampler for 0.1 – 100 uL injection volume, thermostatted (up to 100° C) column compartment, and a variable UV wavelength detector. This instrument is mainly used for small molecule accurate mass analysis, intact molecular weight measurement for proteins and oligos, and simple protein digest analysis.

The LXQ has capabilities similar to the conventional 3D ion trap such as LCQ Deca. It is based on linear ion trap technology that has faster cycle time. It is capable of data-dependent LC-MSn analysis.  This system is equipped with Finnigan MicroAS Autosampler, Surveyor MS pump, and Ion Max ESI source.  Mass spectrometer is controlled by XCalibur data system. The LXQ has BioWorks software, a suite of software for protein identification. The main engine of the BioWorks is SEQUEST protein identification algorithm which automatically comparing tandem mass spectral data (MS/MS) to predicted spectra from DNA databases. The LXQ is used primarily for natural products and proteins analysis.

The Bruker autoflex is a linear time-of-flight (TOF) mass spectrometer equipped with a matrix-assisted laser desorption ionization (MALDI) ion source. It uses a 355 nm Nd:YAG SmartBeam laser.  Among of the main advantages of MALDI-TOF are the "soft ionization" characteristic of MALDI and ease of use. This instrument is routinely used for analysis of organic molecules, natural products, and macromolecules, including recombinant proteins, oligonucleotides, polysaccharides and synthetic polymers. The mass spec facility provides common MALDI matrices including HCCA, sinapinic acid, DHB, HPA.

The 1260 HPLC is used primarily for analytical and semi-prep scale HPLC separation and purification of components in chemical mixtures. This system consisted a quaternary pump, autosampler, thermostatted column compartment, diode array detector (190 – 950 nm), and fraction collector. A Refractive Index Detectors (RID) is available for substances with limited or no UV absorption.

Training Material can be found here.

Contact Information

For questions about the Mass Spectrometry facility and its instrumentation, please contact Lisa Chen, Mass Spectrometer Specialist.