Dr James Hopkins

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Instrument Support Level 4

Instrument Support Level

Instrument Support Level 4

Manufacturer & Model


CEDA Archive Name


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Physical Dimensions

Occupies spaces for two aircraft racks aboard the FAAM aircraft


See page for details

Daily Facility Charge




The aircraft GCMS is capable of reporting mixing ratios of a wide range of volatile organic compounds in the atmosphere. The instrument is designed to be operated aboard the FAAM146 research aircraft and can be configured and operated in a number of subtly different ways to target specific compounds of interest. A brief description of the typical instrument operation is given below, but this may vary depending on the application.

Briefly, Samples of air are drawn, from a dedicated inlet fitted to the window of the aircraft, and pressurised into the instrument using an all stainless steel assembly metal bellows pump. Samples are preconcentrated using a MARKESTT-247 preconcentrator fitted with two identical Tenax-TA adsorbent traps. The preconcentrator is operated such that it collects a sample on one of the adsorbent traps (held at 10 °C typically) while analysing the contents of the other (desorbed at 230 °C typically), thus no time is wasted while the traps are in their cooling phase. During desorption a flow of helium carrier gas is used to transfer the VOCs onto the GC column. At this time a flow of liquid carbon dioxide is directed to the front-end of the column and used to cool it to a temperature of around -67 °C which is sufficient to hold all of the VOCs of interest in this portion of the column for around 30 seconds after which the liquid carbon dioxide flow is stopped and the column rapidly heats up to normal oven temperature and releases the previously trapped VOCs in a small/focussed band which improves the chromatography of the peaks of interest. After separation on the GC column, the VOCs are detected and identified using the quadrupole mass spectrometer.

The aircraft GCMS (gas chromatograph coupled to a mass spectrometer) is used to measure atmospheric concentrations of a range of volatile organic compounds (VOC) for selected deployments of the FAAM research aircraft. The instrument can be operated in subtly different ways depending on the objectives of each study. Here follows a summary of the main aspects of the measurement technique.


Many of the compounds of interest are present in the atmosphere at levels too low for quantitative detection, therefore, large volume sampling involving a concentration stage using an adsorbent trap is required before the samples are analysed.

On-column pre-focussing

As the adsorbent traps (preconcentration stage) are heated to desorb the compounds of interest, they are transferred onto the GC column in a stream of helium carrier gas. The desorption rate (heating rate) of the traps must be rapid in order to transfer the compounds, particularly lightweight/highly volatile compounds, in a short/focussed band which is required for good chromatography. In this particular system the adsorbent traps are large and so the desorption is relatively slow leading to poorly resolved peaks and loss of sensitivity for the volatile compounds. In this instrument liquid CO2 is used to cool the front end of the GC column during the desorption of the adsorbent traps which has the effect of pre-focussing the analytes at the front end of the column. Once the liquid CO2 flow is stopped the column rapidly heats up and the peak shape of the volatile compounds is much improved.

Gas Chromatography

Gas chromatography is a separation method that relies on differences in partitioning behaviour between a flowing mobile phase (carrier gas) and a stationary phase (column coating) to separate the components in a mixture.

Mass spectrometer

Mass spectrometry is a commonly used tool for identification of unknown compounds in a sample. There are many variations in mass spectrometers, but all consist of an ion source, mass analyser and finally a detector.

The source of ions for the aircraft GCMS is from impact of electrons produced by a heated filament (EI). These are accelerated across the ion chamber toward the collector anode. Collision of electrons with organic molecules results in a transfer of energy sufficient to ionise most molecules (10-20 eV). The positive ions and fragments formed are specific to each compound, forming a “fingerprint” for a given molecule, and are passed into the mass analyser by means of a small repelling potential in the source.

The mass analysers used here is a quadrupole mass analyser. Four rods in a quadrant formation surround the beam of ions with opposing rods being electrically connected. Ions of specific mass to charge ratio (m/e) can be allowed to move to the detector end of the instrument, while others can be removed due to the potential difference between the rods.

The MARKES preconcentrator is serviced each year by a qualified engineer. Regular checks are made on the integrity of the traps and these are replaced when deficiencies become apparent.

The instrument is calibrated against a number of different standard mixtures (depending upon the aims and target compounds of each project) which are regularly checked against the calibration scales of the NCAS-AMF dual channel gas chromatograph.


Deployment of the instrument typically requires an NCAS Instrument Scientist operator, in which case the consumables required will have already been arranged by them for the deployment.

Typical consumables required for instrument deployment include:

  • 2 x cylinder of CP Grade Helium (carrier gas) – NOTE: must be 5 litre AV size.
  • 1 x cylinder of liquid withdrawal carbon dioxide per flight – NOTE: must be 5 litre AV size.
  • 1 x cylinder of Nitrogen N6.0 grade (blank gas).
  • 2 x adsorption traps for the MARKES TT-247 pre-concentrator.
  • 2 x replacement filaments for the mass spectrometer.
  • Instrument Insurance
    • This system must be insured by the user for £90K and covers loss, theft or damage to the instrument: damage is that over and above general wear and tear. The system has been designed to be rugged and autonomous. Even so, the end-user must respect the fact that the system is a precision optical instrument that must be treated with great care.
    • The user is responsible for the instrument from the time it leaves the AMOF to the time it is returned and signed off as in an acceptable operating condition by the IS: this will be done as soon as is possible on its return.
  • Public Liability Insurance
    • The AMOF is not liable for any damage or injury arising from the deployment or operation of this instrument when unattended by the IS.
  • Shipping Expenses
    • The user is liable for all costs arising from the shipping of the instrument both to and from a deployment.
  • IS T&S
    • The user is responsible for coving the travel and subsistence expenses of the IS while attending the instrument.

In General, the instrument will be transported and installed on the FAAM 146 aircraft by the Instrument Scientist.

Approximate dimensions of the rack and equipment are:

  • Main Rack:
    • 120 cm (L) x 70 cm (D) x 115 cm (H)
  • Pump tray rack:
    • 95 cm (L) x 75 cm (D) x 60 cm (H)
  • Weight:
    • 300 Kg

Not relevant for this instrument – operates aboard the FAAM 146 aircraft.

Manual handling
  • Replacement of cylinders on the rack poses an obvious manual handling risk. Usual care should be taken when moving such heavy objects.
Electric safety
  • Individual components of the system are commercially available instruments built to a high standard. No attempt should be made to remove the outer covers of the instruments.
Attended operation
  • There is no requirement for the system to be attended during operation from a safety standpoint. However, regular checks should be made to ensure the instrument is working normally and there is normal consumption of gases etc.
Gas cylinders
  • The system requires the use of liquid carbon dioxide from 5 litre cylinders. If there were a large leak of CO2, it may cause suffocation.
  • A CO2 detector is installed on the rack which will alarm if the CO2 levels rise beyond a safe working level. It should be charged-up before and after each flight.
  • NOTE:
    • If a large CO2 leak where to occur, there would most likely be a cloud of condensed water vapour clearly visible so the alarm is merely a precaution. A set of safety instructions is listed on the rack.

The instrument occupies spaces for two aircraft racks aboard the FAAM146 aircraft. One full rack containing the majority of the instrument and one “pump tray” containing the pumps and two 5 litre liquid withdrawal carbon dioxide cylinders.

The aircraft GCMS is capable of reporting mixing ratios of a wide range of volatile organic compounds in the atmosphere. The instrumental method can be set-up in a variety of ways to target particular compounds. Typical target compounds include:

A broad range of hydrocarbons and VOCs (within the range C5 – C12).

Specific hydrocarbons and VOCs (within the range C5 – C12) a limited number at improved sensitivities.

Lightweight halocarbons.

Dimethyl Sulphide (DMS)

NOTE: where calibration mixtures aren’t available for individual compounds – relative differences in mixing ratios can be provided.

Field Data
  • The instrument produces a range of out files and all are text format.
  • The user can download (but not delete) this data from the instrument but it should be noted that this data will not have been quality controlled.
Archive Data