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Proton Transfer Reaction - Mass Spectrometry

The technologies we use in our solutions: PTR-MS, SRI-MS, SRI+...

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

  • ion source
  • drift tube
  • and either a quadrupole or a time of flight mass spectrometer...
A IONICON PTR-MS system consists of...

...three main parts:

Ion source:

Production of H3O+ (optionally also other reagent ions with SRI-MS technology) ions at high purity levels (> 99%) from water vapor in a hollow cathode discharge with the IONICON ULTRA-PURE ion source.

PTR drift tube:

The VOC trace gases in the sampled air undergo (mostly) non-dissociative proton transfer from H3O+ ions, which are injected into the drift tube via a specially designed inlet (pressure in the drift tube ~2.2mbar); alternatively charge and hydride ion transfer or association reactions of NO+ and O2+ can be utilized.

Analyzing system:

  • Quadrupole based systems: A quadrupole mass filter in conjunction with a secondary electron multiplier allows mass separation and detection of the ions.
  • Time-of-flight based systems: A high resolution time-of-flight (TOF) mass spectrometer separates the ions according to their mass to charge (m/z) ratio. The resolution is sufficient to distinguish between isobaric molecules and makes an unambiguous identification possible.


How does an IONICON PTR-MS work?

(using H3O+ as reagent ion)

The fundamental process in a PTR-MS instrument can be written as


This means that protonated water (H3O+) interacts with the trace gas (R). During this interaction a proton transfers from the hydronium to the trace gas molecule, which leads to a protonated and therefore ionized molecule (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). Some other compounds with proton affinities below that of H2O can be detected using our proprietary Selective Reagent Ionization - Mass Spectrometry (SRI-MS) technology.

Click here to see an animation of how PTR-Quadropole-MS works!

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

In the ion source H2O is broken down 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 primary ions and eventually result in a worse detection limit.

The produced protonated water ions are of 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 primary ions and eventually result in a worse detection limit.

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


which can be simplified in good approximation to



In (2) and (3) [RH+] is the density of protonated trace constituents, [H3O+](0) is the density of primary ions (in absence of the neutral reactants [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 densities, 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.

Determination of concentrations
The mass analyzing and detection system (quadrupole mass filter or time of flight mass spectrometer) of the PTR-MS instrument delivers count rates (or currents) 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:


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 real-time.

The combination of the IONICON ULTRA-PURE ion source, the efficient PTR ionization process and a state-of-the-art mass analyzing system 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 O2+
With O2+ compounds are ionized via charge transfer according to equation (5). The recombination energy of O2+ is 12.07eV, thus the electron transfer reaction is exothermic for analytes having an ionization energy below that value.


 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 (6) 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).


For ketones (amongst other reactions) simple charge transfer occurs, which means that the product ions appear exactly on their molecular mass (7).


These facts lead to a situation that with NO+ ionization isomeric compounds appear on different nominal masses and are therefore 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 termolecular association reactions take place and can be used for unambiguous detection.


The simplest form of ionization (charge transfer) with IONICON‘s novel SRI-MS technology is shown in equation (8): the trace compound B transfers an electron to the reagent ion A+. This reaction is feasible when the ionization energy of A is close to or higher than the ionization energy of B.

CTR ohne Fragment.png (8)

However, as CTR ionization is a considerably "harder" ionization method compared to PTR ionization, dissociative charge transfer is much more likely to occur. In equation (9) 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. 

CTR mit Fragment.png (9)

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 (10) and (11) show the two most abundant reactions, namely simple charge transfer (10) and charge transfer with hydrogen abstraction (11).

Benzene mit Kr.png (10)
Benzene mit Kr minus H.png (11)