Characterization of a High Detection-Sensitivity Atmospheric Pressure Interface Time-of-Flight Mass Spectrometer

Schmidt-Ott, Fabian; Maisser, Anne; Lekkas, Alexandros; Papanastasiou, Dimitris; Biskos, George

doi:https://doi.org/10.5194/egusphere-2025-3253

Preprints

https://doi.org/10.5194/egusphere-2025-3253

Preprints

15 Jul 2025

| 15 Jul 2025

Characterization of a High Detection-Sensitivity Atmospheric Pressure Interface Time-of-Flight Mass Spectrometer

Fabian Schmidt-Ott, Anne Maisser, Alexandros Lekkas, Dimitris Papanastasiou, and George Biskos

Abstract. We have characterised a new Atmospheric-Pressure-interface Time-of-Flight Mass Spectrometer, equipped with an octapole ion trap for accumulating the sampled ions before orthogonally accelerating them into the mass analyzer. The characterisation has been carried out using ion standards produced by electrospray ionisation and mobility-selected by a differential mobility analyzer operated at atmospheric pressure. Our results show that the detection sensitivity (or limit of detection) of the mass spectrometer is in the parts per quintillion (i.e., 10^-3 ppq; parts per quadrillion) range with temporal resolutions in the range of 1 second. When increasing the temporal resolution up to 1 minute, the detection sensitivity can be reduced to the 10 parts per sextillion (i.e., 10^-5 ppq) range, enabling the system to measure gaseous ions of extremely low concentrations. In contrast to other mass spectrometers that employ spectra accumulation to improve the detection sensitivity for atmospheric observations, ion accumulation amplifies the signal without increasing the noise level; something that is of significant importance for probing short-lived ionic clusters during new particle formation events in the atmospheric environment, among others. We also show that the mass spectrometer has a transmission of up to 1 %, and a mass resolution of 23,000 for ionic masses of ca. 600 Da., while it can offer collision-induced dissociation of the sampled ions by tuning the operating conditions of the Atmospheric-Pressure-interface stage.

Received: 10 Jul 2025 – Discussion started: 15 Jul 2025

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Fabian Schmidt-Ott, Anne Maisser, Alexandros Lekkas, Dimitris Papanastasiou, and George Biskos

Status: closed

RC1:
'Comment on egusphere-2025-3253', Anonymous Referee #1, 05 Aug 2025
General Comments:
Pushing down the detection limit of APi-TOFs is a significant advancement in atmospheric measurements and is highly relevant for Atmospheric Measurement Techniques. In this manuscript, the authors demonstrate the use of an ion trap (and an ion funnel) to decelerate and accumulate ions before extraction into the TOF-MS, thereby reducing the detection limit below dozens of molecules cm⁻³.
This is an important technical development that could enable the detection of extremely low-concentration species. The setup makes APi-TOFs measuring after DMA possible, for size-selected chemical composition during atmospheric nucleation processes. Therefore, I recommend publication after the following minor revisions.
Specific/Technical Comments:
Page 1, lines 20–21: I recommend changing the unit from ppq to molecules cm⁻³, or showing both, when possible. A major motivation for achieving such low LODs is to probe nucleation events (as authors mentioned), where reporting in molecules cm⁻³ (e.g., 2.5×10⁴ molecules cm⁻³) is more intuitive and widely used than 1 ppq. That said, using ppq occasionally is fine for readers from the gas-phase or trace gas community. I particularly appreciated Figure 2 and line 237, where both units are shown, this is a good practice and should be applied more consistently.

Scientific notation and formatting: Please check the formatting of numbers throughout the manuscript:
Page 1, line 41: change “10.000” to “10,000” (use a comma for thousands, not a dot)

Page 2, line 57: change “10-5%” to correct scientific notation, e.g., “10⁻⁷”

Define abbreviations at first use. Several abbreviations are used without definition:
Page 2, line 64: Define “Ts” here rather than in line 65.

Page 2, line 66: Clarify what “ioniAPi-TOF-MS” means, is this a typo?

Page 2, line 98: Define “DC” at first mention.

Page 4, line 147: Define “THAB”.

Page 5, line 159: Replace the first “TPAI” with “TMAI”, possibly a typo.

Page 3, line 108: Remove “Fig. 1” after “Gate 1”, it is redundant.

Page 5, lines 165–166: Please rephrase this sentence. The LOD is not typically defined as the signal from a single ion striking the detector. Rather, it is defined as the lowest signal that can be reliably distinguished from noise. Your explanation in Supplementary Section S3 is much clearer and more accurate: “The lowest possible signal that the TOF detector of the APi-TOF-MS can measure is that of a single ion striking the detector (Sₐₒₙ).”

Figure 4 and m/z dependence: Figure 4 presents ion transmission for a specific accumulation time (Tₐ). The authors mention extracting ions at three consecutive time points per spectrum to minimize mass bias during accumulation. I wonder whether the trapping efficiency also varies with m/z, for example, low-m/z ions are unstable due to higher kinetic energy or mobility. Could this be dependent on Tₐ as well? Comparing transmission curves for different Tₐ could be insightful and would strengthen the discussion on mass bias.

Page 9, line 312: The authors reference results from Density Functional Theory (DFT) calculations, but note that they are not shown. If possible, please provide a reference to these calculations or supplementary material for readers who may wish to explore them further.
Citation: https://doi.org/10.5194/egusphere-2025-3253-RC1
- AC1: 'Reply on RC1', Fabian Schmidt-Ott, 17 Sep 2025
  
  1. We agree that molecules or ions cm⁻³ is a more intuitive unit and that it should be used more consistently throughout the paper. We have made the necessary changes throughout the manuscript, often providing both units for the better understanding.
  2. We appreciate the comment of the reviewer here. We have changed the formatting to scientific notation.
  3. The ioniAPi-TOF-MS is the APi-TOF-MS produced by Ionicon Analytik GmbH. We have now clarified this my mentioning the manufacturer in brackets. Other proposed changes were made.
  4. The correction has been made.
  5. We agree with the reviewer here. The correction has been made.
  6. The reviewer correctly points out that the trapping efficiency over time in the octapole ion trap potentially varies with m/z. We have not investigated this effect in the current work, but we plan to do so in the near future. A sentence highlighting this point has been added in the updated version of the manuscript.
  7. We thank the reviewer for this point. We have added a new section in the supplement (Section S.5) providing a description of the simulations performed to test the stability of THAB and TPAI. Please note that adding this analysis requires the addition of a new co-author, Dr. Somnath Bhowmick.
  
  Citation: https://doi.org/10.5194/egusphere-2025-3253-AC1
RC2:
'Comment on egusphere-2025-3253', Anonymous Referee #2, 13 Aug 2025
The paper elucidated how they carried out the characterization for atmospheric pressure interface time-of-flight mass spectrometer equipped with an octapole ion trap, where detection sensitivity and ion transmissions are well characterized. I suggest we accept this paper after authors could make some description clearer and add more details.
Comments:
Line 66: typo? What do you mean by ioniAPi-TOF-MS

You should ensure that each abbreviation is defined before it appears for the first time. For example, in line 87, “ESI” is introduced before its meaning is explained, which you explain them in the following section. In Figure 6, the abbreviations “TPAI” and “THAB” are used in the caption, but they are not consistent with those shown in the figure itself.

In Table 1, some units are presented alongside the input parameters, while others are placed with the values. Please make the unit placement consistent throughout the table.

In general, did you describe what kind of solutions that you made for ESI to generate the ions shown in Table 2? I did not find them. I think it is better to include this information in paper.

In line 147, line 256: How did you operate DMS to select single ions with different mass to charge ratio? You only mentioned the parameters to select the THAB monomer, how about others that you listed in Table 1.

Line 198 and 200: Water molecules can also have an effect on the binding energies of ion-molecular clusters, which can help to stabilize the ion-molecular clusters. Please have a look at the paper ‘Computational Comparison of Different Reagent Ions in the Chemical Ionization of Oxidized Multifunctional Compounds’.

In section 3.2. How did you operate the system to define the transmission? What kind of ions with what mass that you used to define the transmission? Do you mean all the ions that you listed in table 2?

Line 315: Is there any reference here?

Line 315-319: What would you obtain in mass spectrum if the dimer ions dissociate? If I understand correctly, I would say, it should be one neutral molecule and one ion-molecule cluster. That means it should not be the neutral monomer in your figure 6. For example, the possible combination should be (C12H28N)2I-, (C12H28N)I- and (C7H16N)I- in panel a, but not (C12H28N)2I-, C12H28N and C7H16N. The same case for panel b.
Citation: https://doi.org/10.5194/egusphere-2025-3253-RC2
- AC2: 'Reply on RC2', Fabian Schmidt-Ott, 17 Sep 2025
  
  1. The ioniAPi-TOF-MS is the APi-TOF-MS produced by Ionicon Analytik GmbH. We have now clarified this my mentioning the manufacturer in brackets.
  2. We thank the reviewer for pointing this out. We have made necessary changes throughout the entire manuscript.
  3. We have made necessary corrections, improving the consistency on how we refer to the units through the manuscript.
  4. We agree with the suggestion of the referee to add the details on the ESI solutions. We have added a relevant part in section 2.2.
  5. We understand that the reviewer here wanted to write DMA instead of DMS, and that parameters for the THAB monomer are the ones provided in Table 2 and not Table 1. The parameters to select monomers and dimers other than THAB was only the potential difference between the two plates of the DMA electrodes. We have modified the text accordingly for clarification.
  6. The reviewer brings up an interesting point, that ion-molecular clusters can be stabilized by binding to water molecules. Since water is presumably absent in our measurements (the electrospray solutions were prepared in acetonitrile), we expect that the effect of water on the binding is negligible in this study. However, for ambient measurement, indeed the stabilization by water molecules can play an important role, where fragmentation of these water-bound clusters is possibly reached at far lower energies than seen in this study. We have included the reference and pointed out, that the presence of water can have a significant effect on binding energies.
  7. This paragraph has now been updated, and addresses the point of the reviewer here clarifying the setting of the API-TOF-MS during the transmission measurements.
  8. Given that referee #1 made a similar comment, we have added chapter S.5 in the supplement providing an in-depth explanation on the simulations performed to test the stability of THAB and TPAI.
  9. We have specified the chemical formulas of possible products of the dissociation of the THAB and TPAI dimers in Figure S-8 in the supplement. Based on comment 2 of the reviewer, we have chosen to change the terminology in the legend to “TPAI” and “THAB” monomer/dimer, making the chemical formulas redundant in Figure 6.
  
  Citation: https://doi.org/10.5194/egusphere-2025-3253-AC2

Status: closed

RC1:
'Comment on egusphere-2025-3253', Anonymous Referee #1, 05 Aug 2025
General Comments:
Pushing down the detection limit of APi-TOFs is a significant advancement in atmospheric measurements and is highly relevant for Atmospheric Measurement Techniques. In this manuscript, the authors demonstrate the use of an ion trap (and an ion funnel) to decelerate and accumulate ions before extraction into the TOF-MS, thereby reducing the detection limit below dozens of molecules cm⁻³.
This is an important technical development that could enable the detection of extremely low-concentration species. The setup makes APi-TOFs measuring after DMA possible, for size-selected chemical composition during atmospheric nucleation processes. Therefore, I recommend publication after the following minor revisions.
Specific/Technical Comments:
Page 1, lines 20–21: I recommend changing the unit from ppq to molecules cm⁻³, or showing both, when possible. A major motivation for achieving such low LODs is to probe nucleation events (as authors mentioned), where reporting in molecules cm⁻³ (e.g., 2.5×10⁴ molecules cm⁻³) is more intuitive and widely used than 1 ppq. That said, using ppq occasionally is fine for readers from the gas-phase or trace gas community. I particularly appreciated Figure 2 and line 237, where both units are shown, this is a good practice and should be applied more consistently.

Scientific notation and formatting: Please check the formatting of numbers throughout the manuscript:
Page 1, line 41: change “10.000” to “10,000” (use a comma for thousands, not a dot)

Page 2, line 57: change “10-5%” to correct scientific notation, e.g., “10⁻⁷”

Define abbreviations at first use. Several abbreviations are used without definition:
Page 2, line 64: Define “Ts” here rather than in line 65.

Page 2, line 66: Clarify what “ioniAPi-TOF-MS” means, is this a typo?

Page 2, line 98: Define “DC” at first mention.

Page 4, line 147: Define “THAB”.

Page 5, line 159: Replace the first “TPAI” with “TMAI”, possibly a typo.

Page 3, line 108: Remove “Fig. 1” after “Gate 1”, it is redundant.

Page 5, lines 165–166: Please rephrase this sentence. The LOD is not typically defined as the signal from a single ion striking the detector. Rather, it is defined as the lowest signal that can be reliably distinguished from noise. Your explanation in Supplementary Section S3 is much clearer and more accurate: “The lowest possible signal that the TOF detector of the APi-TOF-MS can measure is that of a single ion striking the detector (Sₐₒₙ).”

Figure 4 and m/z dependence: Figure 4 presents ion transmission for a specific accumulation time (Tₐ). The authors mention extracting ions at three consecutive time points per spectrum to minimize mass bias during accumulation. I wonder whether the trapping efficiency also varies with m/z, for example, low-m/z ions are unstable due to higher kinetic energy or mobility. Could this be dependent on Tₐ as well? Comparing transmission curves for different Tₐ could be insightful and would strengthen the discussion on mass bias.

Page 9, line 312: The authors reference results from Density Functional Theory (DFT) calculations, but note that they are not shown. If possible, please provide a reference to these calculations or supplementary material for readers who may wish to explore them further.
Citation: https://doi.org/10.5194/egusphere-2025-3253-RC1
- AC1: 'Reply on RC1', Fabian Schmidt-Ott, 17 Sep 2025
  
  1. We agree that molecules or ions cm⁻³ is a more intuitive unit and that it should be used more consistently throughout the paper. We have made the necessary changes throughout the manuscript, often providing both units for the better understanding.
  2. We appreciate the comment of the reviewer here. We have changed the formatting to scientific notation.
  3. The ioniAPi-TOF-MS is the APi-TOF-MS produced by Ionicon Analytik GmbH. We have now clarified this my mentioning the manufacturer in brackets. Other proposed changes were made.
  4. The correction has been made.
  5. We agree with the reviewer here. The correction has been made.
  6. The reviewer correctly points out that the trapping efficiency over time in the octapole ion trap potentially varies with m/z. We have not investigated this effect in the current work, but we plan to do so in the near future. A sentence highlighting this point has been added in the updated version of the manuscript.
  7. We thank the reviewer for this point. We have added a new section in the supplement (Section S.5) providing a description of the simulations performed to test the stability of THAB and TPAI. Please note that adding this analysis requires the addition of a new co-author, Dr. Somnath Bhowmick.
  
  Citation: https://doi.org/10.5194/egusphere-2025-3253-AC1
RC2:
'Comment on egusphere-2025-3253', Anonymous Referee #2, 13 Aug 2025
The paper elucidated how they carried out the characterization for atmospheric pressure interface time-of-flight mass spectrometer equipped with an octapole ion trap, where detection sensitivity and ion transmissions are well characterized. I suggest we accept this paper after authors could make some description clearer and add more details.
Comments:
Line 66: typo? What do you mean by ioniAPi-TOF-MS

You should ensure that each abbreviation is defined before it appears for the first time. For example, in line 87, “ESI” is introduced before its meaning is explained, which you explain them in the following section. In Figure 6, the abbreviations “TPAI” and “THAB” are used in the caption, but they are not consistent with those shown in the figure itself.

In Table 1, some units are presented alongside the input parameters, while others are placed with the values. Please make the unit placement consistent throughout the table.

In general, did you describe what kind of solutions that you made for ESI to generate the ions shown in Table 2? I did not find them. I think it is better to include this information in paper.

In line 147, line 256: How did you operate DMS to select single ions with different mass to charge ratio? You only mentioned the parameters to select the THAB monomer, how about others that you listed in Table 1.

Line 198 and 200: Water molecules can also have an effect on the binding energies of ion-molecular clusters, which can help to stabilize the ion-molecular clusters. Please have a look at the paper ‘Computational Comparison of Different Reagent Ions in the Chemical Ionization of Oxidized Multifunctional Compounds’.

In section 3.2. How did you operate the system to define the transmission? What kind of ions with what mass that you used to define the transmission? Do you mean all the ions that you listed in table 2?

Line 315: Is there any reference here?

Line 315-319: What would you obtain in mass spectrum if the dimer ions dissociate? If I understand correctly, I would say, it should be one neutral molecule and one ion-molecule cluster. That means it should not be the neutral monomer in your figure 6. For example, the possible combination should be (C12H28N)2I-, (C12H28N)I- and (C7H16N)I- in panel a, but not (C12H28N)2I-, C12H28N and C7H16N. The same case for panel b.
Citation: https://doi.org/10.5194/egusphere-2025-3253-RC2
- AC2: 'Reply on RC2', Fabian Schmidt-Ott, 17 Sep 2025
  
  1. The ioniAPi-TOF-MS is the APi-TOF-MS produced by Ionicon Analytik GmbH. We have now clarified this my mentioning the manufacturer in brackets.
  2. We thank the reviewer for pointing this out. We have made necessary changes throughout the entire manuscript.
  3. We have made necessary corrections, improving the consistency on how we refer to the units through the manuscript.
  4. We agree with the suggestion of the referee to add the details on the ESI solutions. We have added a relevant part in section 2.2.
  5. We understand that the reviewer here wanted to write DMA instead of DMS, and that parameters for the THAB monomer are the ones provided in Table 2 and not Table 1. The parameters to select monomers and dimers other than THAB was only the potential difference between the two plates of the DMA electrodes. We have modified the text accordingly for clarification.
  6. The reviewer brings up an interesting point, that ion-molecular clusters can be stabilized by binding to water molecules. Since water is presumably absent in our measurements (the electrospray solutions were prepared in acetonitrile), we expect that the effect of water on the binding is negligible in this study. However, for ambient measurement, indeed the stabilization by water molecules can play an important role, where fragmentation of these water-bound clusters is possibly reached at far lower energies than seen in this study. We have included the reference and pointed out, that the presence of water can have a significant effect on binding energies.
  7. This paragraph has now been updated, and addresses the point of the reviewer here clarifying the setting of the API-TOF-MS during the transmission measurements.
  8. Given that referee #1 made a similar comment, we have added chapter S.5 in the supplement providing an in-depth explanation on the simulations performed to test the stability of THAB and TPAI.
  9. We have specified the chemical formulas of possible products of the dissociation of the THAB and TPAI dimers in Figure S-8 in the supplement. Based on comment 2 of the reviewer, we have chosen to change the terminology in the legend to “TPAI” and “THAB” monomer/dimer, making the chemical formulas redundant in Figure 6.
  
  Citation: https://doi.org/10.5194/egusphere-2025-3253-AC2

Fabian Schmidt-Ott, Anne Maisser, Alexandros Lekkas, Dimitris Papanastasiou, and George Biskos

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https://doi.org/10.5194/egusphere-2025-3253-supplement

Fabian Schmidt-Ott, Anne Maisser, Alexandros Lekkas, Dimitris Papanastasiou, and George Biskos

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Short summary

We characterized a novel Atmospheric-Pressure-Interface Time-of-Flight (TOF) Mass Spectrometer. By accumulating ions in a trap prior the TOF mass analyzer, we achieve a limit of detection in the 10^-3to 10^-6ppq range with temporal resolutions in the order of 1 s to 10 min, respectively. This makes it highly relevant for atmospheric measurements, as it enables probing short-lived, low-concentration species of high importance in atmospheric chemistry and new particle formation.


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