Review of the manuscript “Chemical Ionization Mass Spectrometry Utilizing Ammonium Ions (NH₄⁺ CIMS) for Measurements of Organic Compounds in the Atmosphere” by L. Xu et al. (https://doi.org/10.5194/amt-2022-228)

The manuscript presents a detailed overview of the operation and sensitivity of NH₄⁺ chemical ionization applied in Vocus-type mass spectrometer that uses an improved ion-molecule reactor FIMR. The authors discuss operational constraints, sensitivity calibration as a function of cluster stability (inferred from dissociation voltage inside the instrument) and present detailed comparison of selected species with other CIMS types in the field. The paper is thorough in presenting limitations and advantages of this chemical ionization technique and therefore it will be very valuable for the community. Some comments and suggestions are outlined below.

General comments

While I appreciate how detailed the paper is, I found it quite long as it includes a lot of information: investigations into different instrumental parameters, sensitivity comparison to other instruments as well as CIMS intercomparison in the field. I found few repetitive parts of text that could be shortened to my mind, both between Methods and Results (section 4), and in Supplement. I suggest authors go through the text to try to make paragraphs  shorter and focus clearer. I also found myself jumping between formulas in different parts of main text and Supplementary to get the full picture.

Specific comments

Line 36: Please include Lindinger et al. (1998) and Blake et al. (2006) as references to early NH₄⁺ ionization works.

Lines 46 and 49: Maybe for comparison, report sensitivities in same unit as in your calibrations, cps/ppb?

Equation 10: would be nice to report the value of µ0 used.

Section 3.3. in relation to section 3.2: It would be useful to see the modelled reagent ion distribution for the conditions that were selected for sensitivity characterization? T = 314K, P = 3mbar was used in Section 3.3., was it the same for determining sensitivities in Table 1? It could be mentioned in Methods.

Line 253-254: Authors say that different compounds have maximum sensitivity at different ratios of reagent ions because they have different reactivities “towards NH₄⁺.H₂O and other reagent ions”. What does this mean? Isn’t it so that sensitivity is calculated based only on A.NH₄⁺ and the sensitivity is a function of the cluster stability?

Figure 3: Line colors are so that it is hard to see. Could the compounds be grouped somehow like in Fig. 5, if it is feasible and improves the visibility of lines. How is optimal range determined? By eye, even smaller ratios would be okay.

lines 217-218: Authors say that E/N affects 3 things: reagent ion distribution, focusing effect and declustering. I think in FIMR E/N affects declustering and therefore this regulated reagent ion distribution, so one leads from another. The authors mention just this in the beginning of this paragraph.

Lines 343-346: This already is described in section 2.1. It could be more concise here. And also same text is again in Supplement, section 3.

Figure 5: Could authors specify somewhere why KE_cm,50 is different than in Zaytsev et al. 2019? I assume it is the geometry of the ion-molecule reactor?

Line 425: Could authors clarify what “anticorrelation” mean here? Orange data points and right axis on Figure 6 are absolute CIMS sensitivity and left axis (blue bars) is ratio, so if NOAA H₃O⁺ would have constant sensitivity, I think we would observe similar trend in the ratio as now.

Lines 430-432: A statement that is not necessarily a conclusion from the data presented in this paper. I would suggest to include a reference or remove. Also lines 543-544.

Lines 440-441: Similar as above. Where is it shown in the paper how sensitivity in the presented instrument changes (or doesn’t) with RH? Maybe in Methods, line 104, it is mentioned. Would it be possible to add a figure to SI?

Line 455: Which H₃O⁺ CIMS is this? NOAA?

Line 523: It seems to me that in Figure S13, pentenes peak in early morning.

Line 547: “strong relationship”- maybe worth mentioning exceptions here (like monoterpenes and other).

Equation S6: Are “E” in Eqn. S6 and “E” Eqn. 10 same variables?

Figure S7: If possible, it would be very useful if authors included a table with detected ion compositions in this figure.

Technical corrections

Line 66: Change “Tofwer” to “Tofwerk”.

Line 146: Remove word “does” after H₂O.

Line 164: Authors use I+ in here probably with “I” standing for “ion”, so H₃O⁺ and NH₄⁺. It could be mentioned in the text, just like A is NH₃ and H₂O.

Figure 1: Somewhat difficult to separate solid and dashed lines in the legend.

Line 323: Here, f(NH₄⁺.H₂O) is defined, but it is already used in previous section.

Line 333: Change “k have less uncertain” to “k is less uncertain”.

Line 476: Change “produces” to “produce”.

Line 489: Change “absent” to “absence”.

Line 506: Suggestion to change “as adduct ions” to “as adducts with reagent ions”.

Line 516: Change “a day” to “the day”.

Supplementary line 58: Change “dipoment” to “dipole moment”.

References

Blake, R., et al. “Chemical Ionization Reaction Time-of-Flight Mass Spectrometry: Multi-Reagent Analysis for Determination of Trace Gas Composition.” International Journal of Mass Spectrometry 254, no. 1 (2006): 85–93. https://doi.org/10.1016/j.ijms.2006.05.021.

Lindinger, W., et al. “Proton-Transfer-Reaction Mass Spectrometry (PTR–MS): On-Line Monitoring of Volatile Organic Compounds at Pptv Levels.” Chemical Society Reviews 27, no. 5 (1998): 347–75. https://doi.org/10.1039/A827347Z.

Zaytsev, A., et al. “Using Collision-Induced Dissociation to Constrain Sensitivity of Ammonia Chemical Ionization Mass Spectrometry (NH4+ CIMS) to Oxygenated Volatile Organic Compounds.” Atmospheric Measurement Techniques 12, no. 3 (2019): 1861–70. https://doi.org/10.5194/amt-12-1861-2019.

Review of: A Chemical Ionization Mass Spectrometry Utilizing Ammonium Ions (NH₄⁺ CIMS) for Measurements of Organic Compounds in the Atmosphere

This paper describes the optimization and calibration of a commercially available Chemical Ionization Time of Flight Mass Spectrometer for the measurement of a suite of organic compounds in the atmosphere. Field data from the instrument and comparisons to other instrumentation are also presented. The instrument utilizes NH₄⁺ reagent ions and a relatively new (less than 5 year old design) Focusing Ion Molecule Reactor (FIMR). The authors present the advantages and limitations of using NH₄⁺ chemistry. The paper is very detailed (more on this later) providing more than enough information for other groups to reproduce the results presented here. It is well suited for publication in AMT and will be of great value to the community. That said, I do have a few comments and suggestions below.  

General Comments:

As mentioned above the paper is very detailed. While this is a good thing, there are times this borders on overwhelming and does make the paper quite long. At times I wondered if could be split in two, with the field measurements and instrument intercomparisons being their own paper. The sheer number of species quantified (or estimated using voltage scanning) by the instrument also makes some of the figures difficult to digest. Figure 3 is an example of this. While I understand what the authors are trying to show, the sheer number of traces makes it almost impossible pick out individual species. Anyone suffering color blindness would have no clue what they are looking at. At times, I also found it difficult follow through the jumping around of formulas in the modelling of the reagent ion distribution. Again, I appreciate the level of detail the authors have provided the readers of this paper, I simply feel it should be tightened up in places and presented in a more digestible way.

Specific Comments

Title: I assume the authors meant "A Chemical Ionization Mass Spectrometer Utilizing….." or "Chemical Ionization Mass Spectrometry Utilizing….."

P3 L66: Tofwerk Vocus

P11 Figure 2: A plot of the model results showing the final optimal conditions would be nice to see here somewhere.

P13 Figure 3: As mentioned above this is a very busy plot. I’m wondering if there’s a way the species could be grouped or if the authors could split the plot into panels so that if would be easier to see what is going on. Right now it kind of looks like a mess. 

P14 L281: We have performed……..and measured……

P15 L308: oxygenated aromatics have a…….

P16 L333: …..k have less uncertainty than TE.

P16 L333: You really should not start a sentence with a lower case variable. Perhaps “The value of k……”

P17 L343: This has been mentioned elsewhere and is an opportunity to tighten up the manuscript.

P21 Figure 5: I’m finding it difficult to wrap my head around the sensitivity comparisons between the instruments without taking into account the change in reagent ion signal (sensitivities are cps/ppb not ncps/ppbv). Fluctuations in reagent ions will surely occur. The authors even mention the example of day vs night. I realize this is difficult in the VOCUS instrument since proper counting of the reagent ions puts significant wear on the MCP detectors, but I'm wondering if there is some other way to account for this. 

P22 L476: should be “produce”

P22 L489: Absence?

P23 L516: ….throughout the day.

Supplement

P3 L58: “Further, the dipole moment…..”

P4 Figure S2: Same comments as Figure 3.