Institute for Biodiversity and Ecosystem Dynamics

Chromatography & Mass Spectrometry

Our laboratory are equipped with several liquid chromatography (LC) and gas chromatography (GC) systems. Each system is coupled with a unique detection system, including low or high resolution mass spectrometry, which makes it possible to analyse a broad range of organic chemicals in samples of various origins. In addition to identification and quantitation of chemicals, development of new methodology is an integral part of the services provided by our laboratory.

HPLC-UV/Flu. Photo: Jan van Arkel


Our high performance liquid chromatograph system is equipped with both a general purpose UV detector and highly sensitive and selective fluorescence detector (HPLC-UV/Flu). The system is typically used for the analysis of a wide variety of water soluble compounds within natural samples (e.g. water, soil and plants) or used in degradation or sorption studies. Typical applications include PAH analysis for bioremediation and sorption experiments, plant pigments and toxins, (degradation products of) herbicides and fullerenes, and phenolic acids within soil.

Technical Specifications

  • Chromatography: HPLC Prominence, equipped with a binary LC-20AD pumping system, SIL-20 autosampler and CTO-20 column oven (Shimadzu, Kyoto, Japan).
  • Detection: SPD-M20A photodiode array detector (PDA) and RF-10 XL fluorescence detector (Shimadzu, Kyoto, Japan).

LC-MS/MS. Photo: Jan van Arkel


Our triple-quadrupole like LC-MS/MS system is used for quantitative monitoring of a wide variety of chemicals in the environment. The system is equipped with a highly selective and sensitive tandem mass spectrometer (MS/MS), which can be utilized with different ionization techniques (ESI, APCI and APPI) to analyse a wide range of chemicals. Typical analyses within IBED include monitoring of perfluoroalkyl acids (PFAAs) within water, food and plant material, degradation studies of fullerenes, aryl organophosphorus flame retardants (OPFRs) and several herbicides, monitoring of azaarenes and azaarones within sediment, and the analysis of amino acids within soil.

Technical Specifications

  • Chromatography: HPLC Prominence XR, equipped with a binary LC-20AD XR gradient pumping system, SIL-20AC autosampler, CTO-20AC column oven and CBM-20A controller (Shimadzu, Kyoto, Japan).
  • Detection: 4000 QTRAP MS/MS (Applied Biosystems, Toronto, Canada).

UPLC-QTOF. Photo: Jan van Arkel


A recent addition to our chromatography facilities is our ultra-performance liquid chromatography quadrupole time of flight (UPLC-QTOF) system. The combination of high chromatographic resolution, mass resolving power and mass accuracy, MS/MS and isotopic pattern fingerprinting, allows this instrument to identify and characterize chemicals even within complex sample material. The system can be equipped with several ion sources (ESI, APCI, APPI and IonBooster). Furthermore, Direction Injection Probe (DIP) can be used for direct analysis of both solid and liquid samples. Recent work includes the characterization of (degraded) perfluorinated polymers and screening for degradation products of aryl organophosphorus flame retardants.

Technical Specifications

  • Chromatography: Nexera UHPLC system (Shimadzu, Kyoto, Japan), equipped with a binary LC-30AD gradient pumping system, a LC-20AD dopant delivery pump, SIL-30AC autosampler and CTO-20AC column oven.
  • Detection: SPD20-A UV detector (Shimadzu, Kyoto, Japan) and maXis 4G Q-TOF MS (Bruker Daltonics, Bremen, Germany).


GC-MS system  with both cold-on-column  and split/splitless injectors and the possibility to perform headspace and large volume analysis. Equipped with PAL autosampler.

Used for the analysis of phospholipid fatty acids, lignin, volatile organic compounds such as BTEX, pesticides, brominated flame retardants, PCB’s etc.

Technical specifications

  • ThermoQuest Trace GC 2000 gas chromatograph with Finnigan Trace MS quadrupole mass spectrometer, Milan, Italy

GC-MS system. Photo: Jan van Arkel

Trace GC-MS

GC-MS system with cold-on-column injection and curie-point pyrolysis.

Used for the analysis of free lipids for biomarker research e.g. sterol- and stanol analysis as manure biomarkers, cutin and suberin , brominated flame retardants  etc.

Pyrolisis is used to characterize soil organic matter and plant material. With the pyrolizor unit it is also possible to perform thermally assisted hydrolysis and methylation.

Technical specifications

  • ThermoQuest Trace GC 2000 gas chromatograph with Finnigan Trace MS quadrupole mass spectrometer, Thermo Scientific, Milan, Italy
  • Pyrolyzer: Horizon Instruments Curie-Point pyrolyser, Horizon Instruments, Sussex, England
GC gas

Trace GC Ultra with TCD, ECD and FID detection. Photo: Jan van Arkel

Trace GC Ultra with TCD, ECD and FID detection

Used for the analyses of permanent gasses: carbon dioxide, nitrous oxide and methane in gaseous samples originating from field-sites or lab incubation experiments and for the measurement of acetylene and ethylene in incubated samples.

Equipped with PAL autosampler.

Technical specifications

  • ThermoQuest Trace GC 2000 gas chromatograph with TCD, ECD and FID detectors, Thermo Scientific, Milan, Italy


Membrane Inlet Mass Spectrometry (MIMS)

In our laboratory we have a Hiden HPR-40 Membrane Inlet Mass spectrometer installed with a mass range of 200 amu (atomic mass unit) with a dissolved species probe. This allows for accurate measurements of a wide range of gasses either in gaseous or dissolved in liquid environments. Using stable isotopes specific changes in conditions applied can be quantified. The probe is positioned in a specialised cuvette. Typical applications of the MIMS in our lab are:

  • 13C-labeled bicarbonate or carbon dioxide uptake experiments to quantify rates of carbon fixation in cyanobacteria and algae.
  • 18O2 uptake experiments to quantify oxidation or respiration rates during photosynthesis in cyanbacteria and algae.

Technical specifications:

  • Hiden analytical HPR-40 Membrane mass spectrometer
  • HAL201 RC mass spectrometer with Faraday/Multiplier detector
  • Mass range 200 amu
  • Dissolved species probe type 303416

Published by  IBED

27 November 2017