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The Method, Hardware and Performance of the PTR3

The PTR3 detects volatile organic compounds and their oxidation products including highly-oxygenated organic molecules (HOMs) down to ppqV levels.


Recently, researchers from the Institute for Ion Physics and Applied Physics at the University of Innsbruck have developed a novel concept for a Proton-Transfer-Reaction – Time-Of-Flight Mass Spectrometry (PTR-TOFMS) instrument (Breitenlechner et al., 2017), the so-called PTR3. The fundamental idea behind PTR3 is the decoupling of the ion-molecule reaction chemistry from the axial transport of the reagent and analyte ions. This decoupling allows variations in the E/N without affecting the reaction time. The realization of elevated pressure and increased reaction time tremendously boosts the overall sensitivity of the instrument

As a partner in this original research project we have pursued the PTR3 concept and successfully developed an advanced version of this high performance trace VOC-ELVOC analyzer: The PTR3-TOF 10K. Three ion sources now allow for fast switching of different primary reagent ions, overall ion transmission is further improved and the instrument is completed with a dedicated high resolution TOF-MS - the ioniTOF 10K. 

The PTR3 is a specialized system dedicated to the highly sensitive detection of ultra low traces of volatile organic compounds and their oxidation products that  enables monitoring reactions from the first oxidation steps up to highly-oxygenated organic molecules (HOMs) down to ppqV levels (Breitenlechner et al., 2017). The inlet system and the ionization chamber are especially designed to reduce surface interactions. This concept of contact free sampling allows for detecting organics of virtually all volatility classes ranging from volatile (VOC) to extremely low volatile (ELVOC). 

Recent results from the well-known CLOUD experiment very well illustrate the advantages of the PTR3 over a commonly used nitrate (NO3-) Chemical Ionization Mass Spectrometer (CIMS). Both instruments show a similar detection efficiency towards ELVOCs, but the PTR3 clearly excels the CIMS when it comes to the detection of less oxidized VOCs (see e.g. Stolzenburg et al., 2018; Simon et al., 2020). The ultimate performance of the PTR3 even allows for detecting and quantifying organic peroxy (RO2) radicals. By including these radicals, Hansel et al. (2018) could achieve carbon closure for a cyclohexene ozonolysis experiment when operated in soft adduct NH4+ ionization mode. Furthermore, Zaytsev et al. (2019) recently demonstrated the ability of the PTR3 to study the composition and concentration of secondary organic aerosols.

PTR3 Hardware and Method

Fig. 1 shows a schematic of the PTR3. The dual stage core sampling inlet permits a virtually contact free injection of analytes. Hence, molecules of low vapor pressures like HOMs (even down to ELVOC) are transported into the PTR3 reaction chamber, almost loss-free and without surface interactions.

Primary reagent ions are generated in the revolutionary TRIONSOURCE. Three separate ion sources enable fast electrical switching between a series of different primary reagent ions (e.g. H3O+ , NO+ , NH4+). Each single ion source uses a corona discharge that ionizes the selected chemical ionization (CI) precursor gas. The corona discharge is followed by a short drift region to purify the selected primary reagent ion. Additionally, all three ion sources are separately pumped to minimize interaction of the CI-gas and the sample. These measures result in ultimatively clean ionization modes with lowest interfering background signals.

The heart of the  PTR3 is the patent protected reaction chamber with the enhanced 3D tripole. In conventional PTR-MS technology, the primary reagent ions ionize analytes in a reaction region at low pressure under the influence of an axial DC drift field. Adjusting the reduced electric field strength (E/N) in the reaction region allows to precisely control the ionization energies. In PTR3 however, the 3D tripole is driven by HV-RF voltages creating a rotating field in radial direction that defines the reaction kinetics. Unlike traditional PTR-MS, the axial ion motion is now efficiently decoupled from the electric field. Additionally, the PTR3 is operated at an elevated reaction pressure of 50 to 80 mbar. Since no axial field is present in the reaction region, ions are transported solely by the sample gas flow. This significantly extends the reaction time and subsequently results in outstanding sensitivities while still maintaining IONICON’s patented TRU-E/N ion chemistry. 

The 3D tripole ionization chamber is followed by an ION-BOOSTER funnel that effectively focuses the ions into a hexapole ION GUIDE ensuring optimal ion transmission. 

Subsequently, the hexapole guides the ions into the lens system of the mass analyzer. The mass analyzer itself is a novel high-resolution ioniTOF 10K, achieving mass resolving powers of typically 10,000 to 12,000 m/Δm.

Figure 1: Schematic representation of the PTR3-TOF 10K.

Performance of the PTR3-TOF 10K

Characterization of the instrument shows sensitivities of up to 100,000 cps/ppbV for ketones (i.e. hexanone and octanone) at a mass resolution of 10,000 m/Δm, which can be tuned to up to 12,000 m/Δm. 

The new source design allows for fast electrical switching between a series of primary reagent ions (here, H3O+ and NH4+ chemical ionization modes). An increase of the RF-Amplitude of the 3D tripole ionization chamber clearly illustrates the beneficial impact of the increased E/N on the cluster distribution and charging efficiency. This underlines that the ion chemistry can be precisely controlled even without influencing the reaction time.

Sensitivity and Mass Resolution

Left: Calibration at sub-ppbV mixing ratios (gas standard with 30% accuracy, 26°C, 30% RH, mass resolution of 10.000 m/Δm). Signal intensity is given in counts per second:

Hexanone (m/z 101)   90,000 cps/ppbV

Octanone (m/z 129) 104,000 cps/ppbV

Tripole E/N scan

PTR3-TOF 10k in H3O+ (left) and NH4+ (right) mode at a pressure of 55 mbar in the reaction chamber, the 3D Tripole is operated at a constant RF of 7.5 MHz with increasing peak-to-peak voltages.

Sensitivity and Mass Resolution: Mass resolution in dependency of m/z of the ioniTOF 10k with a resolving power of up to 12,000 (m/Δm) and an exemplary peak system showing 8 well separated peaks.
Tripole E/N scan: Left: Ketones react with all hydrated hydronium ions and clusters (i.e. H3O+(H2O)n; n = 0−3) while limonene only reacts with H3O+(H2O)n (n=0,1). Right: Analytes A are predominantly detected as adducts in the form of A.NH4+. Bond energies of Ketones.NH4+ are lower and dissociate with higher E/N.

Examples of field deployment

Since its invention, the PTR3 has been deployed and successfully tested in various locations and experiments. Some examples are listed below:

  • chamber experiments, e.g. the CLOUD experiment at CERN
  • flow reactor experiments, see e.g. Hansel et al., 2018
  • field experiments: in the Boreal forest of Hyytiälä, Finland; in the Andes of Bolivia

Contact us for more information. Our experts are looking forward to elaborate the benefits of PTR3, addressing your scientific challenges.


M. Breitenlechner et al., PTR3: An Instrument for Studying the Lifecycle of Reactive Organic Carbon in the Atmosphere. Anal. Chem. 89/11 (2017) 5824-5831,

A. Hansel et al., Detection of RO2 radicals and other products from cyclohexene ozonolysis with NH4+ and acetate chemical ionization mass spectrometry. Atmospheric Environment 186 (2018) 248-255,

A. Zaytsev et al., Using collision-induced dissociation to constrain sensitivity of ammonia chemical ionization mass spectrometry (NH4+ CIMS) to oxygenated volatile organic compounds. Atmos. Meas. Tech. 12 (2019) 1861-1870,

D. Stolzenburg et al., Rapid growth of organic aerosol nanoparticles over a wide tropospheric temperature range, PNAS 2018 115 (37) 122-9127;

M. Simon et al., Molecular understanding of new-particle formation from α-pinene between −50 and +25 °C, Atmos. Chem. Phys., 20, 9183–9207,, 2020.