Mass Spectrometry

Mass Spectrometry

The mass spectrometry facility is located in GeoChem Building, Room 408 and consists of:

  • Hewlett-Packard (Agilent) GCD 1800C GC-MS
  • Thermo LCQ Deca XP Max ion trap mass spectrometer with Shimadzu HPLC system
  • Thermo LXQ linear ion trap mass spectrometer with Surveyor HPLC system
  • AppliedBiosystems Voyager DE PRO MALDI-TOF mass spectrometer
  • JEOL JMS-600H double focusing magnetic sector mass spectrometer

Hewlett-Packard (Agilent) GCD 1800C GC-MS

This system is suitable for separation of complex mixtures by gas chromatography (GC) and identification by mass spectrometry.  It is limited to low molecular weight and volatile molecules (mass limit 450 Da). The gas chromatograph routinely employs a HP-5MS capillary column that is useful for separation of most non-polar species.

Thermo LCQ Deca XP Max ion trap mass spectrometer with Shimadzu HPLC system

The LCQ Deca XP Max is equipped with electrospray (ESI) and APCI ionization sources. It is capable of mass analysis of a broad range of molecules that are relatively polar, nonvolatile and thermally labile.  This instrument is used for routine molecular weight determination of compounds from organic, inorganic, natural products, small proteins and peptides, and oligonucleotides.  The LCQ Deca features MSn which significantly increase the performance of LC-MS.  The LCQ Deca may be operated in direct infusion (using the syringe pump from the mass spectrometer), flow injection (inject sample into a LC flow without column separation), or LC-MS.  In direct infusion analysis, the analyte solution is in a syringe and flows to the electrospray source.  The LC-MS is dedicated to microscale analysis of organic synthetic reaction products, natural products, and protein digests..

Thermo LXQ linear ion trap mass spectrometer with Surveyor HPLC system

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 LC-MS applications.

AppliedBiosystems Voyager DE PRO MALDI-TOF mass spectrometer

The Voyager DE PRO is a time-of-flight (TOF) mass spectrometer equipped with a matrix-assisted laser desorption ionization (MALDI) ion source.  It uses a 20-Hz nitrogen laser and the TOF analyzer is capable of operating in linear and reflector modes.  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.

JEOL JMS-600H double focusing magnetic sector mass spectrometer

The JMS-600H is a compact double-focusing, high-resolution, magnetic sector mass spectrometer.  This instrument is equipped with electron impact ionization (EI), Chemical Ionization (CI), and fast atom bombardment ionization (FAB) for characterization of synthetic organic, inorganic, and biological molecules.  For GC-MS analysis, low molecular weight volatile samples are introduced into the ion source using an Agilent 6890 gas chromatograph (GC).  This instrument is also used for routine exact mass measurement of organic molecules. 

The Mass Spectrometry facility is available for use for all faculty, post-doc researchers, graduate and undergraduate students.  All facility instrumentation is available in an open-access manner to trained users, with the exception of JEOL JMS-600H.  New users should schedule time with the mass spectrometrist to discuss their specific mass spec needs and receive training.  For GC-MS and LC-MS walk-up instruments, users will either use the standard columns provided by the facility (GC: 0.25mm x 30m HP-5MS; LC: 2.1 x 50 mm C18), or provide their own columns.

Infrequent MS users as well as off-campus users may submit samples for mass analysis; use the Mass Spectrometry Request Form available via .PDF here or in GC Rm 408 for sample submission.  For research projects that required extensive mass spectrometric analysis, researchers will be trained.  Please contact the mass spectrometrist to discuss training, instrument capabilities, and the most effective use of the mass spec facility.  Assistance will also be provided with data interpretation, advice on sample preparation, experimental designs, and methods development.
A one-day lecture/lab training course for new graduate students is given annually in early January.  The course provides a brief introduction of basics of mass spec and the operation of the mass spec facility, as well as hands-on experience on some instruments.

User fees are charged to cover consumable materials and supplies that are required for routine operation and maintenance of the mass spectrometers.  The current fee schedule for on-campus researchers is $10/hr.

Contact information:
Tun-Li Shen, Ph.D.
Office: MacMillan, rm 313 (tel: 3-2903)
Mass Spec Lab: GeoChem, rm 408 (tel: 3-9779)