BAF has several instruments available for bioanalytical research.

Agilent 1290 Infinity II coupled to ABSciex QTRAP 6500+ with SelexION Differential Mobility
Photo of processors and equipment in a lab
The liquid chromatography tandem mass spectrometry system (LC-MS/MS), depicted in the picture, is composed of an Agilent 1290 Infinity II Ultra High Performance Liquid Chromatography (on the left) which allows high-throughput separation of metabolites based on their chemical properties. The ionization, detection, and quantification of the compounds are carried by a benchtop hybrid triple Quadrupole-Linear Accelerator-trap mass spectrometer.

The ABSciex QTRAP 6500+ mass spectrometer:
  • Is highly sensitive with limits of quantification and detection in the order of femtomole even attomole when multiple reaction monitoring (MRM) is selected.
  • Has a mass range of m/z 5-2000 and can switch from negative to positive ionization within five milliseconds allowing the detection and quantification of metabolites with different polarity in the same run.
  • Is very versatile with a multitude of scan modes such as full scan MS, Product Ion Scan, Precursor Ion Scan, Neutral Loss Scan, MRM, MS3…
  • Can perform two types of ionizations: Electropsray Ionization (ESI) and Atmospheric Pressure Chemical Ionization (APCI).

To complete this state-of-the art LC-MS/MS system a SelexION differential ion mobility (DMS) device is available to resolve metabolites with identical molecular weights, chromatographic retention times, and spectra. SelexION technology uses a very short planar cell that is located behind the curtain plate and upfront of the orifice of the mass spectrometer. Analyst software 1.7 is used to pilot the LC-MS/MS system and analyze data.

Agilent 1290 Infinity II LC coupled to an Agilent 6460 QQQ
Photo of one processor and various equipment in a lab
The Agilent 6460 triple quadrupole mass spectrometer (on the right) is highly sensitive (femtomole level) with a broad mass range of m/z 5-3000. Metabolites of interest are ionized using electrospray ionization (ESI) technology. The scan modes include: full scan MS, MS/MS product ion scan, MRM, neutral loss scan, and precursor ion scan. This instrument is capable of polarity switching within 30 milliseconds simultaneously allowing the analysis of analytes with different polarity. An Agilent 1290 Infinity II Ultra High Performance Liquid Chromatography device (on the left) is interfaced to support fast LC-MS/MS analyses of complex matrices. MassHunter Workstation software is used to pilot the LC-MS/MS system and analyze the data.
Thermo Trace 1310 Gas Chromatography Coupled to an ISQ Single Quadrupole Mass Spectrometer
Photo of equipment and desktop computer in a lab
This instrument is used to analyze compounds (under 1100 amu) that are thermally stable and have a boiling point below 300°C. Metabolites are ionized by Electron Ionization (EI). The autosampler, a TriPlus TSH, permits online derivatization of samples. Possible injections include: liquid phase, headspace and solid phase micro-extraction (SPME). The identification of compounds is performed using NIST 17, a library containing over 300,000 mass spectra.
Technical notes
  • Electrospray Ionization Theory

Electrospray Ionization (ESI) mode creates ions in solution. In the ESI mode, the liquid flow is forced through a stainless steel capillary where a high voltage (3-5 kV) and a nebulizing gas (Nitrogen) are applied. Small charged droplets are generated and undergo a process of solvent evaporation until ions leave the droplets in gas phase. Those ions enter the mass spectrometer to be detected under a specific scan mode. ESI is suitable for polar compounds such as amino acids and phosphorylated compounds.

  • Atmospheric Pressure Chemical Ionization Theory

Atmospheric Pressure Chemical Ionization (APCI) mode creates ions at atmospheric pressure. In the APCI mode, the liquid flow is forced through a stainless steel capillary. Evaporation of both the analytes and mobile phase solvents occur under a heated nebulizer (note that no voltage is applied to the capillary). After nebulization, the analytes and mobile phase solvents are sprayed into a corona discharge needle. As a result, nitrogen is ionized first (most abundant in mobile phase), passes its charge to vaporized solvent, which transmits its charge to the analytes. Finally, ions enter the mass spectrometer to be detected under a specific scan mode. APCI is best suited for metabolites with low to medium polarities.

  • Differential Ion Mobility Theory

After ESI or APCI ionization, ionized metabolites are pushed through a DMS cell (apparatus made of 2 parallel electrodes) using nitrogen as a carrier gas. The separation of the ions is achieved by alternating periods of: i) high voltage for a short amount of time, and ii) low voltage for a longer amount of time. This asymmetric waveform (separation voltage; SV) is continuously repeated across the DMS cell, which causes a drift of the metabolite towards one of the electrode. To compensate for this drift, a direct current voltage (compensation voltage; CoV) is applied to the electrodes in order to guide the ion of interest through the detector of the mass spectrometer. Additionally, chemical modifiers (acetone, isopropanol, acetonitrile, 1-propanol) can be used to enhance the resolving power of DMS.

Instrument Scheduling

Users are required to be trained by one BAF mass spectrometry personnel prior to accessing the mass spectrometer instrument(s). In order to be added to the Outlook calendar corresponding to the mass spectrometer instrument(s) of their choice, the users will receive an invitation by email from the facility's lab manager. At this point, users will be able to login and schedule a time slot on a specific device. Key card access to the facility will be given once the user's training is completed. Please, contact Brier Lee-Renken ( for key card access, and Jean Christophe Cocuron ( for questions regarding mass spectrometer training.


File Attachments

DMS Technology

SelexION Technology