In this work, the authors present measurements of atmospheric cations and anions using an APi-TOF at the SGP site. They further deploy the binPMF to aid the identification of ions and find distinct chemical characteristics and temporal behaviors. The neutral species in the atmosphere that can be inferred from ion measurements have meaningful implications on the atmospheric new particle formation and growth, although quantitative studies require further measurement using active chemical ionization schemes. One main difficulty in understanding ion behaviors is that the abundance of ions is a result of both the concentration of respective neutral species and the charging potential (i.e., proton affinity, molecular polarity, etc.). The authors are fully aware of this complexity and the interpretation in this study is careful and reasonable, which I do appreciate. In general, I think this paper has certainly new insights into the understanding of atmospheric ions at this site and presents an excellent example of what we can learn from ion measurements. Therefore, I recommend the acceptance of this manuscript for publication in ACP, after a few minor concerns are addressed.

Line 21-22. HOMs are spelled as “highly oxidized molecules”, while in Line 44, it is spelled as “highly oxygenated molecules”. I suggest following the definition by Bianchi et al., i.e., “highly oxygenated organic molecules”.

Line 104-105. The authors mentioned that the pinhole of APiTOF was clogged partway through the campaign. I wonder whether there is any influence by the clog, for example on the total ion counts? Please add a sentence about this.

Line 190. For NPF identification, the cut-off size of SMPS is important. The authors mentioned in Line 214 that the low abundance of higher-order sulfuric acid clusters is consistent with the lack of nanoparticles. According to my experience, the sulfuric acid trimer to dimer ratio is always very low (a few %) even in amine-rich environments, so the ratio of 2% here probably can’t be simply taken as indicative of negligible NPF. Could it be possible that SMPS is not able to detect particles down to a few nanometers?

Line 237. The chemical species with m/z located at 288 could also be C5H10N2O8, a widely-observed peak in isoprene-rich environments. The double-bond-equivalent of C10H10O6, as suggested by the authors, seems too high in my opinion. Please double-check the formula assignment on this nominal mass.

Line 292-293. “The increased intensity at odd m/z suggests that neutral organonitrate species clusters with NO3- are more abundant than clusters of HOMs with NO3-”. This statement isn’t right. By definition, organonitrates (with enough oxygen atoms) are a subset of HOMs. Maybe rephrase it as “… than clusters of non-nitrate HOMs with NO3-.”

Line 295-300. I buy that the nighttime NO3+SQT reaction could be strong, but what about the daytime. SQT reacts with O3 fairly effectively, and if the subsequent RO2 reacts with NO, C15 ONs will also be formed. So, I am a bit surprised that no C15 ONs observed during the day. One possibility could be that C15-ONs do not bind with HSO4- as efficiently as it does with NO3-; in this regard, are there any SQT-originated ONs appear in the daytime high-mass factor in the positive ion mode? Another possibility is that the O3 concentration at SGP site is quite low during the day. It would be very helpful if the concentrations of NO, O3, and NO2 are provided. Anyway, please consider rephrasing this part.

Line 301-302. Related to my former comment about NO concentration at SGP site. I’d like to see a short discussion on the reason for the suppressed RO2 cross-reactions. If NO3 is present in a considerable amount, NO concentration has to be very low, which shouldn’t suppress dimer (C30) formation. Maybe this is due to the RO2+NO3 -> RO + NO2 + O2?

I find the discussion on the positive HOM ions a bit unclear. How many HOM-related ions are identified, what are they, and how different are they from the daytime SQT ones and why? I hope to see some discussion on these points.

This study used APi-TOF to measure the ambient ion chemical composition with the newly developed bin-PMF method and scaled Kendrick mass defect. In general, the manuscript is well-written and within the scope of ACP. I would recommend it be published as a measurement report after some minor revisions.

Major aspects

1. In the introduction section, the authors focused too much on the background of atmospheric ion chemistry. Some discussions related to the gaseous vapors from agricultural regions in previous literature are needed. The authors should clearly state the remaining questions related to that field. I noticed some of such discussions are in the results sections but they should also be summarized in the introduction section.
2. It is interesting to see that HSO4- signal is much lower than (H2SO4)HSO4- signal at the measurement site, which is quite different from the existing atmospheric ion studies (e.g., Ehn et al., 2010, Bianchi et al., 2016, and Frege et al., 2017). The HSO4- and NO3- are typically the predominant ions in the negative ion spectra determined from APi-TOF observation in the aforementioned studies because of their relatively abundant parent neutral species (HNO3 and H2SO4 in the day). Thus, a detailed explanation/discussion may be needed here, especially since the authors mention that fairly abundant HNO3 concentrations are expected (line 233) based on the PMF results.
3. The authors observed evident levels of C15 compounds (CHOs and CHONs) and attribute a substantial fraction of them to sesquiterpene-related HOM in the “high m/z nitrate factor”. While a substantial level of sesquiterpene can be emitted from the herbaceous crops around the measurement site, direct observational evidence (e.g., sesquiterpene measurements) may be needed to support such a conclusion.
4. Similarly, the authors conclude that more insight into NPF precursors can be provided by applying bin-PMF based on APi-TOF dataset. While this may be true, no NPF event has been observed/reported in this study. More evidence is required to support such a conclusion. Some background information such as pre-existing particles and NOx can also be added in SI.
5. As the authors suggested, the bin-PMF could be a very useful tool in analyzing APi-TOF data in the future. The authors should explain more clearly how it is conducted with Tofware, which could be quite important information for potential Tofware users. Also, the peak list of the ions, the corresponding neutral species, their potential sources, and the average mass spectra from different trajectory sectors would also be needed in SI.

Other comments:

Line 229: What is the reason for the nighttime HSO4- signal?

Line 357: What is the diurnal variation of the total ion counts of the observed negative ions?

Figure 5: The difference between the signal fraction of each m/z is not evidently shown in the figure. A different color code in the log scale is recommended here.

Line 482: Why m/z 240 is removed before doing bin-PMF? A further discussion is expected here (Section 3.4) according to the method section (Line 131).

General comments

This manuscript presents ambient ion composition measurements from the Southern Great Plains. The analysis does not lead to very far-reaching conclusions, but ambient ion composition is a result of a multitude of factors, and as such analyses tend to be more qualitative than quantitative. That being said, the analytical methods are very appropriate, the results are presented in a clear and logical fashion, and the conclusions are to the point. I enjoyed reading the manuscript and only have a few minor comments for the authors to consider before final publication.

Specific comments

• Line 32: Does one of the references discuss examples of how ions can “affect neutral gas-phase chemistry through ion-neutral interactions”? It does not sound like a very common reaction mechanism, and therefore it would be interesting to hear more explicitly what kind of reactions are referred to here.
• Line 102: Would be useful to state also the length of the 10mm tube, though I expect it to be very short.
• Line 105: The clog of the inlet is acknowledged, and the impacts are discussed in different parts of the manuscript. While I don’t expect that there will be any impact on any of the conclusions in this work, it would be useful to add a bit more discussion about the topic. In particular, since on line 131 in the SI it is stated that the primary effect would be lowered signal, I feel that there is a risk that readers might underestimate the potential severity of such a change. For one part, if the SSQ pressure is not controlled to be constant, a change in inlet flow would change the pressure in this (and subsequent) chambers, potentially causing large changes in mass-dependent transmission and declustering strength. The authors should state whether this pressure was controlled or not. Even in the case of an unchanged pressure, the dynamics of the expansion from the pinhole will change, and potentially again affecting the same properties (in addition to the absolute signal strength, which the authors already mention).
• Lines 122-125: While I am quite familiar with these subjects, I still have a hard time understanding the message of either of these two sentences, in particular the second one. Please try to reformulate. Is “stable isotopes” the correct term here? Why exactly is redundant information minimized?
• Line 136 onward: Since the authors clearly know the peak shape and resolution functions from Tofware, it is not clear to me why these are not used, instead of the method outlined in this paragraph. I expect the results would be nearly identical, but I feel it would be good state the reason for this approach.
• Lines 149-150: This is stated as a general truth here, but there is no a priori reason why this should always be the case. If this sentence was a conclusion based on the authors own data, it should be said more clearly. I also think there is a word missing in the sentence.
• Section 3: Concerning the naming of factors, I believe the “nitrates” factors are named based on them being clusters with NO3- (?), but “nitrates” is also used in relation to organic nitrates. I suggest to go through the manuscript to make sure that every usage of “nitrate” is unambiguous concerning which type of nitrate compound is meant. I also suggest to avoid using terms of the type “negative/positive binPMF factors”. Since the “P” already stands for positive, there is the risk for confusion. I suggest to always include the word “ion” or “mode” after positive/negative. This includes the SI, where e.g. “positive binPMF” is used several times.
• Line 257: “Formulas are presented as clusters with the nitrate anion”. Do you mean that you did not remove the (potential) NO3- from the given formulas?
• Lines 292-293: This sentence confuses me. Organic nitrates can also be HOM, so what is actually being compared?
• Lines 296-297: This conclusion may be true, but it may also be due to the ON not clustering as efficiently with bisulfate, or that bisulfate just prefers to cluster with other species.
• Line 302: The lack of dimers is very intriguing, and I would like to see some speculation on the reasons. To my knowledge only NO has been shown to kill dimer formation, but since the authors suggest NO3 oxidation to be important, the NO should be very low.
• Lines 400-402: If pyridine has a lifetime of 40 days, it should be quite well mixed vertically as well, so why would BL dynamics deplete the signal?
• Lines 455-459: I don’t understand why this scaling will result in differences between odd and even masses.

Technical corrections

• “SGP” is used in the abstract before it is defined.
• Line 128: The use of “either” seems misplaced?