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GC-Triple Quadrupole Mass Spectrometer (GC-MS/MS)


This platform is dedicated to the highly sensitive, quantitative, and targeted analysis of small molecules The standard set-up is used to analyse non-volatile compounds (mostly primary metabolites). The system is equipped with a sample preparation robot that is capable of automated online TMS derivatisation procedure especially suited for non-volatile compounds including amino acids, organic acids, mono- and disaccharides.

The analyses is done by a technique called multi reaction monitoring (MRM), where only specific target mass ions are selected by the first quadrupole and subsequently fragmented by the second quadrupole, to obtain a set of “daughter” mass ions. These “daughter” mass ions are highly specific for a particular analyte of interest. The third quadrupole is then used as a scanning device or mass filter. This allows a very sensitive detection of analytes even in complex sample matrices with a high dynamic range. 
Next to the MRM analysis of target compounds the system can be run in full scan mode, simultaneously enabling the untargeted analysis of target and non-target compounds, including spectral matching of unknowns with mass spectral libraries (e.g., NIST 14).

Technical Details

The system comprises a Thermo Scientific GC-MS/MS consisting of a Trace 1300 GC with a PTV injection unit. The GC is equipped with a Deans heart cutting module to selectively remove unwanted analytes from the chromatogram. The GC is connected to a TSQ8000 Duo triple quadrupole mass spectrometer from Thermo Scientific Instruments. At the forefront a Thermo TriPlus RSH autosampling robot is installed.

Further Specifications

Trace GC 1300

  • PTV injector programmable with max. 15 °C/sec up to 450 °C
  • Deans heartcut module
  • Ready for one extra injection or detection system


  • ExtractaBrite electron impact ion source cassette
  • Mass range: 1.2-1100amu
  • Scanning speed: up to 20,000amu/s
  • Dynamic range: up to 7 orders of magnitude
  • Simultaneous multimode acquisition (SIM, SCAN, SRM)
  • Timed SRM function for efficient multi-compound analysis

TriPlus RSH injection robot

  • Heated agitator for 6 samples
  • Custom made sample tray for up to 220 samples
  • Automatic syringe exchange system
  • Automated online MeOX/TMS derivatisation procedure


  • Targeted analysis of primary plant metabolites with relation to stress, resistance, crop quality, adaptation, etc.
  • Untargeted metabolomics analysis with relation to e.g., plant-environment interactions, disease biomarkers, biosynthetic and signalling route elucidation, etc.

Complementary Techniques

We also offer platforms for GC-MS volatile and LC-MS non-volatile analyses which are fully complementary to this TSQ approach.

Last edited by Oscar de Vos on 2020-10-07

Our expert(s)
Roland Mumm
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Wageningen Plant Research
Shared Research Facilities


BIOS Applied Metabolic Systems

To explore the potential of nature to improve the quality of life.

This Shared Research Facilities equipment database offers researchers from universities, research institutes and companies, including start-ups, the opportunity to find research equipment with their relevant expert and to use it, generally on a pay-per-use basis. The equipment is available at different locations at Wageningen Campus or other (company) locations. If you want to share your own research devices or if you need more information, please contact us.