Ionisation and Detection of Organic Molecules

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 ~1×10^-4mbar. 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

If you are interested in a particular compound and want to know whether it is suitable for PTR-MS analysis, the first thing is confirm that it has a proton affinity greater than that of water (691kJ/mol). We have provided a list of commonly used compounds with proton affinities greater  than that of water sorted by name.

The Kore PTR-TOF-MS is delivered with a water vapour system that produces H₃O⁺ reagent ions from the ion source, but the glow discharge ion source can be operated with other gas species. Alternative gases can be supplied to the glow discharge ion source as a standard instrument feature.

O₂⁺ Reagent Ions

These ions can be generated by passing pure O₂ gas into the glow discharge ion source. It is also the case that allowing air to the glow discharge will also produce copious amounts of O₂⁺. Also produced with an air feed are NO⁺ ions, but the ionisation energy for this species is 9.26eV, as opposed to 12.07eV for O₂⁺, and thus the dominating ionisation method for most analytes is by charge exchange with O₂⁺.

BTX sample in water (ppm level) with O₂⁺ reagent ions. Note how the molecular ions are M⁺ species, not (M+H)⁺, as is observed with H₃O⁺ reagent ions.

NO⁺ Reagent Ions

NO gas can also be fed directly into the glow discharge, where it produces an intense beam of NO⁺ ions at mass 30 (see above). The low intensity peaks at mass 31 and 32 are due to ions ¹⁴N¹⁷O and ¹⁵N¹⁶O, and ¹⁴N¹⁸O and ¹⁵N¹⁷O respectively.

Ar⁺, Xe⁺, Kr⁺ Reagent Ions

We have also operated the Kore glow discharge source on various noble gases such as argon, xenon and krypton. In this mode, the ion source is run on an inert gas such as argon, xenon or krypton, instead of N₂/H₂O mixture.

The primary ion produced from the glow discharge source has a specific energy in its ionised state. If it impacts a molecule in the collision cell and that molecule requires less energy to be ionised, then that molecule can become ionised and the primary ion will convert to a neutral particle. The sequence is as follows:

Kr⁺ (13.99 eV) + CO → CO⁺ (13.98 eV) + Kr
(Chemical Ionisation by Ion-Molecule Reaction)

However, if the molecule requires more energy than is available in the rare gas ion, the molecule remains neutral, e.g.

Kr⁺ (13.99 eV) + N₂ → Kr⁺ + N₂
(No Chemical Ionisation)

This is because 15.5 eV is required to ionise N2.

Notice that N₂ and CO both have masses of 28. Their exact masses are 28.0061 and 27.9949 respectively. Ordinarily, a mass spectrometer would need to have a certain ‘resolving power’ to separate these two masses. However, by using a chemical ionisation technique, it is possible to achieve selective ionisation of such ‘isobaric interferences’.

Ionisation energies of inert gases that can be run in the glow discharge source:

The glow discharge has been run with both Ar and Xe, producing Ar⁺ and Xe⁺ ion beams Krypton may also be used.

The table below lists the ionisation energies of various components, and the primary ion beams that could be used.

Ionisation Energies of Common Compounds

Organic molecules have lower ionisation energies. In a collision, if the difference in ionisation energy is large, then the excess energy can cause fragmentation of the organic molecule. Thus the ionising gas species should be matched where possible to the analyte molecules of interest. For this reason, some researchers also run a primary ion source on Hg vapour to produce Hg⁺ ions (10.44eV) to minimise fragmentation.