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This page provides a technical overview of the physical and chemical principles driving Proton Transfer Reaction – Mass Spectrometry (PTR-MS). It details hydronium-based chemical ionization kinetics for selective VOC detection and examines how RF ion funnels and hexapole guides optimize ion transmission to the TOF analyzer and explains how maintaining well-defined reaction conditions ensures precise, fragmentation-free compound quantification.

An IONICON PTR-MS system consists of 3 main parts: 

  • Ion Source
  • Drift Tube
  • Mass Spectrometer.

How does an IONICON PTR-MS work?

(using H3O+ as reagent ion) 

Ion Source

For efficient chemical ionization via reaction (1) an abundant supply of H3O+ ions is necessary. In IONICON PTR-MS instruments these reagent ions are generated in a dedicated ion source that was developed and has been continuously improved to perfection over many years by our renowned experts.

In the ion source H2O vapor is ionized and fragmented in a hollow cathode discharge. In a second step the fragments recombine to protonated water ions (H3O+) with very high purity (up to 99.5%) and can therefore be injected directly into the PTR drift tube without the need of an interconnected mass filter, which would lead to an inevitable loss of reagent ions and eventually result in an inferior detection limit.

PTR drift tube

The fundamental process in a PTR-MS instrument is

H3O+ + R → RH+ - H2O   (1)

This means that protonated water (hydronium; H3O+) interacts with the analyte (R). During this interaction a proton transfers from the hydronium to the analyte, which leads to a protonated and therefore ionized product ion (RH+) and a neutral water molecule (H2O). The proton transfer reaction is energetically possible for all VOCs with a proton affinity higher than that of water (166.5 kcal/mol). Many further compounds with proton affinities below that of H2O can be detected using our proprietary Selective Reagent Ionization – Mass Spectrometry (SRI-MS) technology.

In the PTR drift tube the actual chemical ionization process (1) of the analytes takes place. It can be easily derived that the PTR process (1) follows the equation

[RH+] = [H3O+]0 (1 - e-k|R|t)   (2)

which can be simplified in good approximation to

[RH+] ~ [H3O+]0 |R|kt    if

[RH+] << [H3O+] ~ [H3O+]0 = const.   (3)

In (2) and (3) [RH+] is the density of protonated trace constituents, [H3O+]0 is the density of reagent ions (in absence of the analytes [R]), k is the reaction rate coefficient and t the average time the ions spend in the reaction region. The assumption (3) is justified, because only molecules with a Proton Affinity (PA) higher than the PA of water (166.5 kcal/mol) undergo a PTR reaction. As all common constituents of ambient air (N2, O2, Ar, CO2, etc.) have a lower PA than water, the air itself acts as a buffer gas and only volatile organic compounds (VOCs), which are usually present in very small concentrations, get ionized. Compared to electron impact ionization, the energy transfer in the PTR process is very low. This effectively suppresses fragmentation and leads to mass spectra that are easy to interpret.

Mass Spectrometer

Subsequent to the PTR drift tube and prior to the mass spectrometer there is a differentially pumped ion transfer region. In basic PTR-MS instruments this region consists of a conventional lens system. In more advanced models there are two types of ion focusing devices, which suppress ion losses during the transfer and thus improve the instruments' sensitivity and lower the detection limit.

Ion funnel

Ion funnels are RF devices which have been used for decades to focus ion currents into narrow beams. In some PTR-MS setups of competitors the focusing properties of the ion funnel improves the sensitivity of the setup for a few compounds by a factor of >200 (compared to operating in DC only mode, i.e. with the ion funnel turned off), whereas the sensitivities of other compounds are only improved by a factor of <10. That is, because of the highly compound dependent instrumental response one of the main advantages of PTR-MS, namely that concentration values can be directly calculated, is lost and a calibration measurement is needed for each analyte of interest. Furthermore, with this approach unusual fragmentation of analytes has been observed which complicates interpretation of measurement results and comparison between different types of instruments even more.

In IONICON PTR-MS instruments the ion funnel is not predominantly part of the reaction region but mainly for focusing the ions into the transfer region to the Time-Of-Flight (TOF) mass spectrometer. This enables a considerable increase in sensitivity and thus also an improvement of the detection limit, while keeping the ion chemistry well-defined and thus avoiding problems with quantification and interpretation of the results.

Ion guide

Quadrupole, hexapole and other multipole ion guides can be used to transfer ions between different parts of an instrument with high efficiency. In PTR-MS they are particularly suitable for being installed in the differentially pumped interface between the reaction region and the mass spectrometer. While quadrupole ion guides are known to have high focusing power, but also rather narrow m/z transmission bands, hexapole ion guides have excellent focusing capabilities over a much broader m/z band. Additionally, less energy is put into the transmitted ions, i.e. fragmentation and other adverse effects are less likely to occur. Consequently, IONICON's latest high-end PTR-MS instruments are equipped with hexapole ion guides for considerably improved performance or even with a sequential arrangement of an ion funnel followed by a hexapole ion guide for even higher sensitivity and lower detection limit.

TOF mass analyzer

IONICON's in-house built orthogonal acceleration TOF mass analyzers are equipped with ion mirrors for highest possible mass resolution. The ions injected from the PTR drift tube via the transfer region are pulsed in packages into the field free TOF region. The time ions need to travel along the flight path depends on their m/z, i.e. by precisely measuring the flight time of each ion in the package, high resolution mass spectra are obtained within split-seconds. A microchannel plate is used for detecting the ions with utmost sensitivity.

Determination of concentrations
The mass analyzing and detection system of the PTR-MS instrument delivers count rates which are proportional to [RH+] and to [H3O+]. The average time t can be calculated from system parameters (drift voltage, pressure, temperature, etc.) and the reaction rate coefficient k can be found in literature for many substances (alternatively it can be calculated or experimentally determined). Knowing all necessary variables in (3) makes it possible to calculate the concentrations of VOCs in the measured volume of air without the need of gas standards via equation:

[Concentration]ppbv = C * [RH+] / [H3O+]   (4)

The highly sophisticated PTR-MS software automatically acquires and calculates all necessary data for equation (4) (constant C which includes k, t and a conversion factor as well as the ratio of the signal intensities) so that the user can monitor the absolute concentrations in ppbv or pptv of all measurable VOCs in online and in real-time.

Conclusion
The combination of the IONICON ULTRA-PURE ion source, the efficient PTR ionization process and a state-of-the-art mass analyzer in an IONICON PTR-MS instrument offer the possibility to monitor and quantify VOCs down to the single-digit pptv range while being compact, low cost in maintenance and reliable for a wide field of customers.

Selective Reagent Ionization – Mass Spectrometry (SRI-MS)

Ionization with NH4+

As an alternative to H3O+ already in early PTR-MS related publications the use of NH4+ reagent ions has been suggested. Ammonia has a proton affinity of 853.6 kJ/mol. For compounds that have a higher proton affinity than ammonia proton transfer can take place similar to the process described above for hydronium:

NH4+ + R → RH+ + NH3   (5).

Additionally, for compounds with higher, but also for some with lower proton affinities than ammonia a clustering reaction can be observed

NH4+ + R → R•NH4+   (6)

where the cluster needs a third body to get collisionally stabilized. The main advantage of using NH4+ reagent ions is that fragmentation of analytes upon chemical ionization is strongly suppressed, leading to straightforward mass spectra even for complex mixtures. The reason why during the first 20 years after the invention of PTR-MS NH4+ reagent ions have only been used in a very limited number of studies is most probably because the NH4+ production required toxic and corrosive ammonia as a source gas. This led to problems with handling the instrument and its exhaust gas, as well as to increased wear of vacuum components. IONICON recently invented a novel method of NH4+ production without the need of any form of harmful ammonia. In this method N2 and water vapor are introduced into the hollow cathode ion source and by adjusting electric fields and pressures NH4+ can be produced at the same or even higher purity levels than H3O+. This invention, which eliminates all problems connected to the use of NH4+ so far, but preserves all advantages of this unique reagent ion.

Ionization with O2+


With O2+ compounds are ionized via charge transfer according to equation (7). The recombination energy of O2+ is 12.07eV, thus the electron transfer reaction is exothermic for analytes having an ionization energy below that value.

O2+ + R → R+ + O2   (7)

This means that with O2+ it is possible to ionize molecules that cannot be ionized via proton transfer from H3O+ because of their low proton affinity.

Ionization with NO+


Ionization with NO+ offers the great ability to identify and separate several isomeric molecules. When aldehydes react with NO+ very likely hydride ion transfer takes place. Equation (8) describes this process and it can be easily seen that for this mechanism the product ions will appear on their molecular mass minus one amu (because of hydrogen loss).

AH + NO+ → A+ + HNO   (8)

For ketones (amongst other reactions) simple charge transfer occurs, which means that the product ions appear exactly on their molecular mass (9).

AH + NO+ → AH+ + NO   (9)

These facts lead to a situation that with NO+ ionization isomeric compounds appear on different nominal m/z in the mass spectrum and are therefore easily distinguishable.
Note: NO+ ionization is nearly as soft as proton transfer from H3O+, which means that fragmentation is considerably suppressed. In addition to charge transfer and hydride ion transfer sometimes association reactions take place and can be used for unambiguous detection.

SRI+

With IONICON's patented SRI+ (US9188564B2, EP2606505B1) reagent ions can be utilized which possess a higher recombination energy than O2, which transforms PTR-MS into a universal trace gas analyzer. One of the most important SRI+ reagent ions is Krypton (Kr) with a recombination energy of 14 eV. That is, charge transfer can occur to all compounds with an ionization energy below 14 eV, which includes virtually all common compounds. Formula (10) shows the charge transfer process with the analyte B which transfers an electron to the reagent ion A+.

A+ + B → A + B+   (10)

However, as charge transfer ionization is a considerably "harder" ionization method compared to PTR ionization, dissociative charge transfer is much more likely to occur. In equation (11) the reagent ion is again A+, whereas the trace compound B consists of C + D. As a result of the reaction only the charged fragment D+ will be detected at the mass spectrometer. 

A+ + B → A + C + D+   (11)

One example, where both reaction pathways can be observed is the charge transfer ionization of benzene (C6H6) with Kr+ as the reagent ion. The equations (12) and (13) show the two most abundant reactions, namely simple charge transfer (12) and charge transfer with hydrogen abstraction (13).

Kr+ + C6H6 → Kr + C6H6+   (12)

Kr+ + C6H6 → Kr + H + C6H5+   (13)

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