The manuscript by Leppla et al. investigates the chemical composition and potential sources and chemistry of organic aerosols in two different wet and dry seasons in the Amazon rainforest with the deployment of an UHPLC-HR-Orbitrap mass spectrometer. It also compares the molecular composition and volatility of background compounds with relatively low variability and compounds with higher variability. The topic of this manuscript is very interesting. However, some revisions are needed before its possible publication on ACP. Please see my comments and questions below.

Major:

More discussions on the comparison of the results at different heights are needed as the abstract underlined the height-resolved measurements. If the chemical composition is similar at different altitudes (Line 366-367, 390-392), then it seems not so important to include all heights in the main text (?). Is there any nocturnal differences in chemical composition below and above forest canopy? Could the authors comment on this?

Specific:

Line 29-30. The reviewer didn’t find the results in the main text on the forest canopy height being the main source of biogenic emissions or early terpene oxidation products. Wet season 2018 seems to have the filters collected at the closest height (40m) to the canopy height (35m); however, Wet season 2018 had less compounds (both background and variable ones) in Figure 2 and 3. 

Line 105-106. Could the authors explain the purpose/reason of sampling at different heights in wet and dry seasons (e.g. wet season 2018 at 42m and 150m but dry season at 0m and 80m)? How would this affect the result interpretation and comparison between different seasons? Could the authors comment on this?

Line 111. How many filters were collected at each height and each season? Please add this information.

Line 132-134. Why did the authors exclude fluorine in the data evaluation if recent studies have found fluorine-containing species in Amazon? Are they present in your dataset? What’s their signal intensity contribution? Considering the high resolution of Orbitrap, it should be possible to identify fluorine-containing species, unless they are not present in this study.

Line 186-188. What did the authors mean in terms of “Only compounds that were observed in more than 75 % of all samples were defined as background compounds”? Is it based on the presence of the compound in the samples or based on some concentration criteria?

Line 188-190. Are the remaining compounds unidentified compounds since the variable compounds are the remaining species of the total identified compounds from the background compounds? Would be nice to add total numbers of identified compounds for all groups (background compounds, variable compounds, and remaining compounds), and more importantly their signal intensity fraction.

Line 196-202. Please add the signal fractions of compounds with MW below 250 Da, 300-450 Da, and above 450 Da correspondingly. Also a typical mass spectra would be very informative.

Line 208-211. Would be nice to add the compound subgroup contributions from the mentioned remote/suburban/urban environments in the literature. Also the elemental ratios obtained in this study in Line 216 could be added.

Line 297. Which figure or table showed this? Please specify. Also considering important contributions of biogenic emissions during the wet season, could the authors explain the reason why the intensities of a-pinene oxidation products were higher in the dry than in the wet seasons?

Line 343-344. Why did 2019 dry season have fewer HOM? Is it related to the higher NO levels or more fires during this period?

Line 378-386. Would be nice to have a table for variable compounds similar to Table S2 (for background compounds) in SI. Also since the authors separated daytime vs nighttime for the variable compounds, why didn’t you do the same for background compounds as well? Or is there no difference for day vs night for background compounds?

Line 393-395.

- If the authors would focus only on compounds with high intensities in the five areas, the reviewer would suggest to have a table for them similar to Table 2, and label them in Figure 3 similar to Figure 1.

-Also C5H12O7S was already discussed in the background compound in Table 1. The reviewer would assume it should not be present in the variable compound group here as well. Same for C5H6O4 in Line 427 which was also listed in Table 1.

Line 459-463. Do you mean the dry season 2018 (in Line 459) had higher levels of CHON species at night than day? Is it a typo? It doesn’t seem to be the case for wet season since there were very few CHON species both day and night. 

Line 468-473. What’s the dominant species for these combustion-related highly unsaturated organic compounds?

Line 520-525. Would be nice to have similar plots for the year 2019 data in SI. Also for background compounds from section 3.2.

Line 526-529. The authors know the molecular formulae of the compounds with MW between 500-600, and therefore it's possible compare the dominant species to the sesquiterpene oxidation products from Gao et al., 2022.

Line 547-548. Would be nice to have similar plots for the year 2019 data in SI as those in Figure 6 and 7. Also for background compounds from section 3.2.

Line 581. Based on the discussions e.g. in Line 480-481 that the wet season 2019 was significantly influenced by biomass burning and combustion activities (Figure S11), the reviewer is wondering whether the wet season 2019 can still be classified as “clean” periods. Also the 7-d HYSPLIT backward trajectories in Figure S3 also shows the wet season 2019 had contact/source from the African continent but not the case for the wet season 2018.

Figure 5. Please change the y axis of lower panels from contribution of number of compounds” to “contribution of signal intensity” (Volatility Basis Set VBS; Donahue et al., 2006), since histogram of number of compounds doesn’t equal to their role in volatility.

Technical:

Line 46. Would change “their nucleation” to “their oxidation products’ nucleation”.

Line 83-84. Seems repetition with the sentences in the previous paragraph.

Line 84-86. Also seem a bit repetition with the sentences in line 80-81. Please consider combine them.

Line 201. Change “ions” to “molecules with MW”.

Line 236. Change “particle phase” to “particles”.

Line 262-322. Please consider removing the bold headlines (e.g. “General”, “Isoprene SOA”) in each of the paragraphs. Also the case for the bold headlines in section 3.3.1 for the five classes.

Line 336. Change “nuclei” to “clusters”.

Line 358. Typo for LV-OOA. Same for Line 452: typo for SV-OOA. Also Figure 4.

Line 477-478. Seems repetition with the previous sentence.

Line 599. Change “what” to “which”.

Table 1 and S2. Change “Signals” to e.g. “Number of compounds detected”.

Reference:

Donahue, N. M., Robinson, A. L., Stanier, C. O., and Pandis, S. N.: Coupled partitioning, dilution, and chemical aging of semivolatile organics, Environ. Sci. Technol., 40, 2635–2643, 2006.

本研究调查了从 2018 年和 2019 年几个季节从亚马逊雨林收集的有机气溶胶的分子水平化学特性。Orbitrap MS 数据显示了有关有机分子的大量信息，对该领域的读者具有深刻的见解。我建议作者解决以下评论：

主要评价：

尽管作者在摘要中强调了垂直分辨抽样的使用，但正文缺乏对不同抽样高度下结果的充分比较和讨论。如第 366-367 行和第 390-392 行所示，不同海拔高度的化学成分似乎大致相似。如果确实如此，则有必要进一步解释在多个高度采样的基本原理。目前，结果并未完全证明高度分辨测量的科学价值。建议笔者从以下几个方面加强讨论：1.夜间或特定气象条件下采样高度之间是否存在可观察到的化学差异？例如，森林树冠上方和下方的化学成分是否会因气溶胶沉积、垂直混合或局部化学反应而出现夜间差异？2.如果总体差异最小，这是否表明研究区域存在强烈的垂直混合或稳定的边界层结构？对此的讨论将有助于解释观察到的垂直均匀性。3.高度分辨采样是否仍然在识别潜在的源区域、反应机理或沉积过程方面提供价值？鼓励作者在他们的结果中进一步讨论这个问题。

具体评论：

1. 第 80 行：虽然该研究包括在多个高度进行采样，但引言并未明确阐明这种垂直采样设计的科学原理或目标。鉴于大气成分、光化学过程和污染物转化会随海拔高度而显着变化，因此必须阐明为什么选择不同的高度以及这对总体研究目标有何贡献。
2. 第 105-110 行：每个季节在每个海拔高度收集了多少个过滤器？请添加此信息。
3. 第 185-186 行：手稿将“背景化合物”定义为在超过 75% 的样本中观察到的化合物。然而，目前尚不清楚这种分类是如何确定的。它是仅基于匹配的分子式，还是还考虑了 MS² 数据来确认结构相似性？由于具有相同分子式的化合物可能具有不同的结构和性质，因此阐明用于此定义的标准非常重要。我建议作者在方法部分明确描述这方面，以确保透明度和可重复性。
4. 第 196-198 行：这里的描述是摘要吗？结论基于哪个数字或表格？
5. 第 208-210 行：最好在文献中包括来自偏远/郊区/城市环境中复合亚群的具体贡献。
6. 第 246-247 行：鉴于 CHONS 仅占 1%，将其视为主要组成部分似乎值得怀疑。
7. 第 275-280 行：手稿讨论了不同 NOx 条件对反应机理或产物分布的影响，但并未明确定义用于区分高 NOx 和低 NOx 条件的标准。此外，本研究中观察到的实际 NOx 浓度并未在正文中说明。我建议作者清楚地说明分类标准并提供这项工作中使用的 NOx 数据，以提高讨论的科学严谨性和可重复性。
8. 第 409-411 行：异戊二烯衍生的有机硫酸盐 （OS） 通常是通过光化学氧化形成的，导致白天的浓度高于夜间。然而，在这项研究中，观察到的 CHOS 化合物在夜间显示出更高的丰度。建议作者更清楚地强调异戊二烯 OS 的主要形成途径，以加强夜间浓度超过白天水平的结论的基本原理和可信度。
9. 第 416 行和第 430 行：请在附录中说明使用了多少标准化合物和哪些标准化合物，并说明每个标准确定了或确认了哪些物质。
10. 第 598-600 行：先前的研究表明，土壤中的有机硫排放量随着土壤湿度的增加而增加，这表明在雨季期间，森林土壤来源可能更强。因此，建议作者进一步探索 CHOS 和 CHONS 的垂直分布是否受土壤排放的影响——尤其是在夜间或稳定的边界层条件下。从下到上递减的浓度梯度可以支持这一假设，并将加强对 CHOS/CHONS 化合物形成和来源归属的讨论。