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Click here to download a Powerpoint file of a presentation made at a recent U.K. conference using this instrument

Example data from PTR TOFMS

The following example data was collected using the PTRMS mode on the PTR/CI/APCI TOFMS built for Nottingham University, as a quick demonstration of the "GCMS" mode of data collection. In this mode a list file is created of all ion arrival events occurring during the experiment. The list file also contains markers for each TOF cycle start, which typically occur every 30µs. Following the measurement, the data are processed into a set of mass spectra, where the collection time per spectrum and the number of bins per mass unit in each spectrum can be selected according to the time resolution and dynamic range required. The resulting data set is the same format as a conventional GCMS dataset where the "chromatogram" displays some time variant aspect of the experiment, movement of the sampling tube in the example below. It is convenient to use the language of GCMS, which many researchers are familiar with, even when there is no chromatograph column involved.

By choosing a time of flight mass spectrometer, all masses are collected, preserving the maximum amount of information. Chromatograms can be created from single ion signals or combinations of ions. These decisions can be left until after the experiment and based on the results. Of course obtaining good chromatogram resolution and reasonable dynamic range simultaneously requires high sensitivity, which is provided by Kore's Proton Reactor and source coupling optics. The only fundamental limit on chromatogram resolution, other than the requirement for adequate statistics, is the basic time of flight mass spectrometer cycle, which is typically only 30µs in this instrument.

The list file, containing all the data from the experiment below occupied about 23Mbyte in raw form, or less than 10Mbyte in zipped form.

Full Mass Spectral Acquisition in 0.1 Second Time Slices

The following experiment was performed:

  1. Two drops of a fabric softener were placed into a 10 cc glass vial
  2. Two drops of a cola beverage were placed into a 10 cc glass vial
  3. The PTR-MS instrument acquisition was started using the "chromatogram mode"
  4. The inlet capillary was placed in the neck of each glass vial in turn, with a small time gap in open air between each sampling
  5. The acquisition was stopped after 20 seconds.

The data set consists of a stream of data that can be analysed retrospectively. We chose to 'replay' the data using a 100ms integration time (each mass spectrum contains data acquired in just 100ms of elapsed experiment time).


From the 'total ion chromatogram', we could see variations in the total ion signal.


We extracted a mass spectrum from the first intense peak in the total ion chromatogram (at approximately 4 seconds), and observed that the data was the same as that acquired from a separate headspace measurement of cola.


Likewise, we extracted a mass spectrum from one of the negative-going peaks in the total ion chromatogram (at approximately 7 seconds), and this corresponded to sampling the fabric conditioner. Each spectrum covers the full range of mass and is generated from only 100ms of experiment time.

Animated gif of sequence of spectra

This small movie shows the most informative section of the spectrum changing in real time. The movie is displayed here mostly for a bit of fun, but playing in real-time here (see time marker) it does illustrate the speed of this instrument.


Next, we selected single mass peaks at 93 and 47 that appeared to be characteristic of the cola and the fabric conditioner respectively. These peaks are identified by crosses on the mass spectra. From the data set we then extracted the single ion chromatogram traces for those peaks. The cola trace is in purple and the fabric softener trace is in green.

Clearly we could have 'sliced' the data into 50ms time slices and still had plenty of signal to easily distinguish the two compounds, but in this case there was no advantage as the chromatogram resolution was limited by the simple manual sampling method.

In this experiment the choice of a single mass peak for each compound chromatogram is perfectly adequate. An obvious extension for a more complex situation would be to use multivariate techniques, such as principal component analysis, to exploit the information available across the full range of masses that TOF MS makes available. This would further improve the dynamic range and allow discrimination between compounds with more subtle differences in the mass spectrum. Having made the analysis to identify a principal component mass vector, it is a simple matter to create a corresponding chromatogram.

This simple experiment hints at the incredible power of a TOF-MS to perform real-time mass spectrometry across the full mass range (parallel detection) with time resolution down to at least 100ms.


Last updated: 12:19 19/02/2014

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