General Comments:

Zang & Willis present an instrument characterization study of a Vocus CIMS, switching between H₃O⁺ and NH₄⁺ reagent ions for the purpose of detecting and quantifying a large range of reactive organic carbon compounds with a single CIMS. They investigate and optimize their ion-molecule reactor conditions for each reagent, present methodologies for quantifying hysteresis timescales when switching reagents, and demonstrate their capabilities via ambient measurements of fresh and oxidized biogenic emissions. I believe this manuscript will serve as a solid foundation for new Vocus users who aim to use reagent switching. Many of my specific comments are meant to clarify details for such readers. I recommend this manuscript for publication following edits in response to the following comments.

Specific Comments:

Line 9 – Specify the integration time for the LODs (I believe 1 s?)

Line 74 – The back reaction can also be important if the reaction is only slightly exothermic (e.g., HCHO in PTR).

Line 110 – Specify the model of Vocus.

Section 2.1 – Please include your fIMR and BSQ settings (amplitude and frequency) since they will also influence your sensitivities.

Line 127 – Rather than have the reader rely on the figures, list the full ranges of fIMR pressure and front voltage used in your experiments here as well. Also provide the corresponding, nominal E/N range.

Line 137 – Please provide the nominal E/N for each set of parameters.

Section 2.3 – When calculating sensitivities, did you observe / account for interfering ions? For example, I find that the monoterpenes, including limonene, fragment to the C₇H₉⁺, toluene’s quantitative ion.

Section 2.3 – A table in the SI with the observed fragments (and their abundances) would be useful for others attempting to characterize their own instrument.

Section 2.3 – Were any of the fragments you observed affected by the BSQ transmission attenuation? If so, did you correct for mass transmission when calculating fragmentation rates?

Section 2.3 – In my experience, fragmentation seems to have a significant dependence on voltage gradients throughout the instrument (e.g., between the Vocus back voltage and the BSQ skimmer; or that same skimmer and the BSQ front voltage) in addition to the fIMR conditions. Have you investigated this dependence? If not, it may be prudent to note some of those gradients in your optimized setups for anyone attempting to recreate those conditions.

Section 2.3 – Was there a reason you settled on 60 °C (PTR is typically higher, ~80-100 °C)? To promote NH₄⁺ adducts? Higher temperatures are commonly used to limit adsorption, so would higher temperatures improve the hysteresis timescales?

Line 170 – Which ion optics do you change? I don’t believe there is any discussion of changing e.g., BSQ or PB settings in Section 3.1 or the methods. From line 315 (“… changes in the BSQ mass range”) it sounds like there was a change, unless I’m misunderstanding.

Section 3.3 – You note humidity independence based on your results. Broadly, I agree. However, I highly encourage addition discussion of the minor humidity dependence at the highest humidities as shown in Fig. 4 (NH₄⁺ ~5% higher at 50% RH, ~10% higher at 70+% RH – except for alkenes). NH₄⁺ appears to have a stronger dependence than H₃O⁺? Can you comment on compound-related trends?

Line 318 – The analyte ion was chosen due to persistence, but does it provide a representative hysteresis timescale for most/all analytes? Have you attempted to repeat this process with other analytes and do they yield similar results? Are there other considerations readers should be aware of when picking analytes/internal standards?

Line 319 – You mention that ambient variability may impact the derivation of hysteresis timescales. Have you performed the calculation in the absence of averaging (i.e., calculate the timescale for each reagent switch individually) to get a sense of the variability? If I were to apply the average hysteresis timescale to the whole campaign, is there a concern that some switches would have longer timescales that impact interpretability?

Line 323 – Do you have recommendations for reagent switching timescales? Can you comment on striking a balance between rapid switching to monitor more ROC vs longer dwell times to minimize the data loss to hysteresis?

Lines 324-325 & Fig. 5e – Figure 5e took a while to understand. I kept trying to compare it to the purple traces in Fig. 5a-d. I think additional explanation in Section 3.4 on how to interpret Figure 5e would be beneficial for the reader.

Line 326 – Also provide the % data lost for each reagent, since it is asymmetric.

Line 404-405 – Reiterate the threshold you used here. Also note the data retention for each ion chemistry due to the different timescales.

Figure 3 – The background shading is distracting. It took me a moment to realize they didn’t represent data. I think the color coding of the standards’ names is sufficient.

Figure 3 – I would typically associate “Molecular Ion Fraction” with A*H⁺ and A*NH₄⁺ (i.e., inaccurate terminology for the fragments and clusters). Perhaps something closer to “Fractional Signal Contribution”?

Figure 6 – How many ions are included in this plot?

Table S3 – Specify sensitivities are for NH₄⁺.

Figure S4 – Expand the H₃O⁺ panel y-axis so the dashed lines are more apparent.

Technical Comments:

Line 282 – Capitalize first word.

General Comments:

In this manuscript, Zang and Willis present the development and evaluation of a method for switching between the reagent ions, NH₄⁺ and H₃O⁺, in a Vocus-CI-ToFMS to detect reduced and oxygenated gas-phase reactive organic compounds (ROC). They detailed the optimization of ion-molecule reactor conditions for both reagent ions, compared their ability to detect a variety of ROC species, and applied the NH₄⁺/H₃O⁺ reagent-ion switching to the ambient measurements in a rural pine forest. Compared to CIMS measurements that employ complementary reagent ions either with repeated experiments or using different instruments, switching reagent ions in a single instrument as described in this study avoids the interferences from the changing inlets and instruments and enables a better evaluation of the capabilities of different regent ions in detecting ROC species. Overall, this work is solid and well designed, and the manuscript is nicely written. I recommend the publication of it in AMT after the following minor comments are addressed.

Specific Comments:

Line 127: Please also specify the default settings of fIMR pressure and front voltage here.

Line 140: Please provide the RH range evaluated here.

Line 152: The ambient air was sampled using a 4-m long PFA tubing. Was the wall loss of ROC compounds significant in the sample inlet, especially for the oxygenated ROC?

Line 244: “Comparable” is not appropriate word here, as for many oxygenated ROC species shown in Figure 2, H₃O⁺ exhibits significantly higher sensitivity than NH₄⁺ .

Line 263: Not only 2-octanone, but also acetone. In Figure 3, only the molecular ion fraction of 2-hexanone is displayed for ketones. Suggest adding other ketones such as hydroxyacetone, methyl ethyl ketone, and methyl vinyl ketone to the figure, which also have a lower detection limit in NH₄⁺ mode than in H₃O⁺ mode.

Line 264-265: The authors stated that “reduced fragmentation has a larger impact on sensitivity between the two reagent-ions for more highly oxidized compounds with multiple functional groups.” However, the H₃O⁺ ionization induces stronger fragmentation while having higher sensitivities to all ketone species, compared to the NH4+ ionization. Please modify this statement.

Line 270: As shown in Figure 4, ion signals of several species show a small but noticeable positive dependence on the RH for both reagent ions. This phenomenon should be mentioned and the reason should be discussed.

Line 281 and Figure 5: Although the authors mentioned in the text that the influence of H₃O⁺ reagent ions were not observed in NH₄⁺ mode, it would be good to also plot the signal profiles of an example protonated ROC species in Figure a-e or in a separate figure.

Line 331: This comment is also related to Figure 5. As shown in Figure 5a, there remains a non-negligible fraction of NH₄H₂O⁺ ion signals after switching the reagent ion to H₃O⁺ for 300 s. Do the residual NH₄H₂O⁺ ions in H₃O⁺ mode contribute to the ionization and detection of the highly oxygenated ROC species that are undetectable with H₃O⁺ in ambient measurements?

Review of “Deployment and evaluation of an NH+4 /H3O+ reagent-ion switching chemical ionization mass spectrometer for the detection of reduced and oxygenated gas-phase organic compounds” by Zang et al.

The authors presented a very nice characterization and application study of chemical ionization mass spectrometry (CIMS) using both ammonium and hydronium ions as reagent ions in the Vocus time-of-flight (ToF) CIMS. Automatic switching between these two reagents was realized and applied in a field campaign at a forested site. The results showed that although these two methods can detect most of VOCs studied (in total 23), hydronium ion (as in PTR-ToF-MS) is more suitable for reduced VOCs, while ammonium ion is more suitable for functionalized VOCs (S/IVOCs). A method was proposed to filter the periods with hysteresis during reagent ion switching, and field data were used to evaluate the performance of this method with auto-switching of reagent ions. The study is well designed and conducted, and the manuscript is clearly written. The findings are valuable in atmospheric chemistry research community in that it provides a method that can efficiently measure a wide range of VOCs and S/IVOCs in the atmosphere. I therefore recommend publication after Minor Revision, with some comments as follows.

Main:

1. The only concern I have is on the criteria of setting the time periods of data to filter out during the hysteresis due to reagent ion switching (section 3.4). In addition to the reagent ion (ammonium-water adduct), the author also chose the C3H6O-ammonium adduct to get the decreasing/increasing rates by taking the derivatives. And it seems that the authors preferred to use the results from the C3H6O-ammonium adduct to determine the time periods of data for filtering (comparing Figure 5 and L325). I have reservation on this for two reasons. First, it is indeed okay to assume that the constituents leading to the signal of C3H6O-ammonium adduct do not change within the 15 min of reagent ion switching. But one might not have good reasons to assume that the proportions of the C3H6O species in the air sampled (presumably acetone and propionaldehyde?) remain the same in the 550+ hours of data (2000+ decreasing/increasing curves used in Figure 5b and 5d). I assume that the ionization efficiency (or sensitivity) of acetone and propionaldehyde might differ with ammonium CIMS, or the authors can convince me otherwise. If so, and if their proportions in the C3H6O species changes, the shape of the exponential curves in Figure 5b and 5d) will be substantially distorted after averaging, thereby resulting in a high uncertainty in the estimation of the time for data filtering. The second reason is that by looking at Figure 5, the ammonium-water ion has both obvious exponential shape and its normalized signal intensity can restore to 1 in the switching from hydronium ion to ammonium ion (Figure 5c); the C3H6O-ammonium adduct ion, however, cannot restore even after 300 s (Figure 5d). Therefore, a better justification and clarification of choosing the data C3H6O-ammonium adduct ion instead of ammonium-water adduct ion to determine the time for data filtering are needed.
2. For the field data, the authors only used the average mass spectra to compare the signal-to-noise ratios of ammonium and hydronium ionization results. It would be good to show some comparison of selected species for both ionization methods to demonstrate the applicability of this method. That is, it is good to show that sensitivity of certain compound classes might different with different reagent ion, but the quantification results are still comparable. In addition, Figure 6 is a bit too difficult to distinguish the differences for those with small signal-to-noise ratios. It would be better to show results in bar charts for those series of compounds with different oxygen atoms that are generally in accordance with the discussion in the text (L346 onward).

Minor:

L70: “A” should be no charge on it as a neutral analyte?

L172-173: this looks like two sentences.

L195: “evident from” or “different from”?

L282: “Reagent-ion chemistry”?

Subsection title of 3.5: “Reagent-ion comparison”?