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Basic Principles of PTR: Ionisation and Detection of Organic Molecules

The Kore PTR-TOF-MS instruments are chemical analysis tools that combines a proton transfer reactor (PTR) with a time-of-flight mass spectrometer (TOF-MS) to make a PTR-TOF-MS.

Proton transfer is a 'soft' chemical ionisation method that allows a neutral gas molecule, such as a low concentration analyte in air, to be ionised without significant fragmentation of the molecule. This contrasts with other ionisation techniques such as electron impact (EI) that cause molecules to fragment, thus creating complex mass spectral patterns.

The most common form of the proton transfer method uses a 'primary' or 'reagent' ion beam of H3O+, i.e. a water molecule with a proton attached. The 'proton affinity' of H2O is 691kJ/mol. If a protonated water molecule (known as 'hydronium') collides with another gas molecule and the proton affinity of that neutral molecule is greater than 691kJ/mol, then the proton is transferred. The ionisation cross-section is practically the same as the collision cross-section. Such a molecule is now charged and can be focused electrostatically and then measured in a mass spectrometer for characterisation. The common constituents of air (N2, O2, Ar, CO2) all have proton affinities less that water, and these molecules are not ionised by this method. Most organic molecules have proton affinities greater than water and are ionised with little or no fragmentation. This makes the technique very suitable to the characterisation of volatile organic constituents in air, although of course the technique is not limited to air analysis and other molecules such as hydrogen sulphide (H2S), hydrogen cyanide (HCN) and ammonia (NH3) can be detectable by this H3O+ PTRMS method.

The H3O+ ion beam is created in an ion source, in Kore's case a hollow cathode glow discharge source, and then injected into the transfer reactor at ~1mbar pressure. Under the influence of an electric field and also the viscous flow of the gas, the ions travel through the reactor. Analyte gas is injected into the reactor, and the molecules undergo collisions with the H3O+ ions. Protons are transferred where this is energetically favourable. This PTR drift section has a set of parallel plate electrodes defining a field gradient, and the ions move toward the end of the PTR section under the influence of that field. The value of the electric field divided by the number of molecules gives the Townsend Number (E/n). When the E/n value is high, the analyte molecules can collide too energetically and fragmentation results. However, if the E/n ratio is too low, water molecules in the primary beam begin to form clusters and these are less effective at ionising the analyte molecules.

It is typical for the method to operate with a large excess of H3O+ ions compared to the concentration of organic species in the analyte sample, so that losses of protons from the H3O+ population are negligible and the H3O+ population is essentially constant. The relationship between the counts of analyte vs. analyte concentration is thus linear through to ~50ppm concentration.

The ionised organic molecules emerge from the reactor at ~1mbar pressure into a lower pressure region at ~1 x 10-4 mbar. At this pressure, the flow changes from viscous to molecular flow, and conventional electrostatic ion optics can be used to extract the divergent ion beam and focus the ions into the mass spectrometer. At this stage the ion beam is still continuous. In the next section of the instrument, the TOF ion source, the ion beam is converted into a pulse of ions suitable for the time-of-flight method. Typically a pulse of ions is extracted from the beam at intervals of ~20-50 microseconds. The extraction pulse is initiated by a high performance time-to-digital converter (TDC) designed by Kore, and the pulse of ions then travels in and out of the reflectron analyser to an ion detector. Within each cycle, the light ions arrive at the ion detector first, followed by successively heavier ions. The ion arrival signals are timed to an accuracy of 0.25 nanosecond. This arrival time is converted by software into a mass (strictly a mass/charge ratio). If the repetition rate is 20kHz (50 µs cycles), then in a ten second measurement there are 200,000 cycles in which data is accumulated into a mass spectrum.

Below is a table of proton affinities for various gaseous components. Any molecule with a proton affinity less than that of water will not be ionised by H3O+, and either other PTR reagents with lower proton affinities such as NO+ or O2+ or other ionisation methods such as electron impact ionisation or chemical ionisation by ion-molecule reactions (Ar, Kr, Xe) need to be used to ionise those components.

Proton Affinities for Common Analytes
Species Name PA
(kJ/mol)
He Helium 178
Ar Argon 369
O2 Oxygen 421
H2 Hydrogen 422
N2 Nitrogen 493
NO Nitric Oxide 532
CO2 Carbon Dioxide 541
CH4 Methane 543
N2O Nitrous Oxide 550
HCl Hydrochloric Acid 557
NO2 Nitrogen Dioxide 591
CO Carbon Monoxide 594
O3 Ozone 625
C3H8 Propane 626
COS Carbonyl Sulphide 628
SO2 Sulphur Dioxide 672
C4H10 Butane 677
H2O Water 691
C2H5Cl Ethylene Chloride 693
H2S Hydrogen Sulphide 709
HCN Hydrogen Cyanide 712
C6H6 Benzene 750
CH3OH Methanol 754
C2H5OH Ethanol 776
C4H6 1, 3 Butadiene 783
C7H8 Toluene 784
PH3 Phosphine 785
C8H10 Ethyl Benzene 788
C8H10 p-Xylene 794
NH3 Ammonia 854

If you are interested in a particular compound and want to know whether it is suitable for PTRMS analysis, the first thing is confirm that it has a proton affinity greater than that of water (691kJ/mol). The NIST Chemistry WebBook has proton affinities for a very large number of compounds. You may search by name or by formula. When available the proton affinity is listed under "ion energetics". Alternatively, here is a list of compounds with proton affinities greater than that of water sorted by name. You can use your browser text search (usually available by typing Ctrl F) to help you find compounds of interest.

For applications where the energetics of the hydronium ion are not suitable, other reagent ions can be created and used. Here are some alternatives.


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Last updated: 16:59 17/02/2014

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