MS: Mass Spectrometry

DCIF Mass Spectrometer Instrumentation

Fourier Transform Mass Spectrometer

The Facility houses a Bruker Daltonics APEXIV 4.7 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (FT-ICR-MS), controlled by a Windows 2000 PC workstation. Ionization sources include electrospray (ESI), electron impact (EI), and direct analysis in real time (DART). The spectrometer is equipped with a Agilent auto sampler to assist in high throughput ESI analysis. 

Sample submission:

  • Place sample (~ 0.5mg) in a small sample vial. Solids are preferred but liquids are OK. Do not use a plastic vial if the samples are only soluble in chloroform or methylene chloride.
  • Chemistry Department Researchers should fill out a mass spectrometric analysis request form (download one in .pdf form here) and submit the samples. If your sample is unstable under room temperature conditions, you may leave the sample on the bottom shelf in the DCIF's refridgerator or keep the sample in your lab and the DCIF Mass Spectroscopist will notify you when the experiment is ready. Researchers may request several scan variations so if you are unsure, you are encouraged to discuss analysis details with a member of the DCIF.
  • The currently installed ion source (EI, ESI, and DART) and projected usage dates are listed on the white board at the entrance to the DCIF.
  • Please note!! To verify which ionization source was used for your sample analysis look at the file name on the bottom of the spectrum. The nomenclature is as follows:
    File name: xxx/data/XX/XXxxxx_ESI, Source: Electrospray ion source (ESI)
    File name: xxx/data/XX/XXxxxx_EI, Source: Electron Impact and Chemical Ionization (EI/CI)
    File name: xxx/data/XX/XXxxxx_DART, Source: Direct Analysis in Real Time (DART)
  • An FTMS services guideline can be downloaded here.
  • The terms "High resolution", "Exact mass", "Mass accuracy" and others are used almost interchangeably.


Gas Chromatograph/Mass Spectrometer

The DCIF has an Agilent 5973N Gas Chromatograph/Mass Spectrometer (GC/MS) - This is a student operated unit mass, electron impact GC/MS. This instument is good for volatile, neutral molecules up to ~500amu. 

  • A training sheet for the new GC/MS can be downloaded here.
  • After downloading the training sheet, use the Training Request Form to schedule an appointment.
  • For nostalgia puposes we have retained our graphic Hewlett-Packard MS ChemStation Tour. It will only take a few moments but it will help you become familiar with some of the features along with the now somewhat outdated Windows 3.1 software interface before training. Click here to take the tour.

Bruker Omniflex MALDI-TOF

The DCIF has a Bruker Omniflex MALDI-TOF instrument with a Reflectron accessory. This instrument is ideal for unit mass determination and structural analysis of non-volatile organic compounds (with N, O, S or aromatic rings), bio-molecules, polymers, proteins, and many other molecules in the ~600 to 60,000 amu mass range (possibly higher). The instrument is student operated. In order to gain instrument access users must be trained by the DCIF mass spectroscopist.


The MALDI-TOF training's are divided into two separate sessions.

  • The first sessions will focus on sample preparation and can accommodate up to four (4) students. These sessions will also address the proper handling / preparation of the MALDI targets and further address issues concerning the different matrices and calibration standards. These sessions are critical as proper / careful sample preparation is of the utmost importance in a MALDI-TOF experiment. The sample preparation session must be completed before you start the instrument operation session.
  • The second session will concentrate on instrument function / features / and operation. These sessions can only accommodate two (2) students.


  • The DCIF does not supply targets, matrices, or calibration standards but does have a few targets that groups may "check out" until a group acquires their own target(s).
  • The MALDI targets are available from Bruker for ~$220.
  • Matrices and calibration standards are available from various sources (including Bruker) and prices may vary anywhere from ~$200 to $500 depending upon the compounds desired.
  • If you would like to be trained, see the Training Request Form to schedule an appointment.

Get a MALDI training sheet here and a MALDI sample preparation sheet here .

Waters Q-TOF Micro Mass Spectrometer

The DCIF has a Waters Q-TOF micro mass spectrometer on open access to researchers. The Q-TOF is equipped with an ESI (electrospray ionization) ion source, a TOF (Time of Flight) detector, secondary mass (MS/MS) utility, and an Agilent 1100 auto-sampler. Q-TOF analysis is suitable for organic polar compounds with molecular weights up to 10,000 daltons. Samples must be soluble in water or an organic solvent such as methanol, acetonitrile, acetone, ethyl acetate, dichloromethane, or chloroform. The Q-TOF is ideal for obtaining unit mass data. Exact mass results require an internal calibration.

See the Training Request Form to schedule an appoinment.

Training sheets and sample prep information will be posted in this space soon.