This manuscript presents results from aerosol filter samples taken at various altitudes that were then analyzed for organic compounds using chromatography followed by orbitrap MS. The mass spectrometer had sufficient resolution to identify atomic formulas. There was both a broad analysis for unknown compounds and a targeted analysis for a few compounds of interest, such as PFAs. These are some of the first measurements with this level of analytical detail of organic aerosol at high altitudes.

The manuscript is interesting and well written. I suggest some revisions:

1) The science issue that I see is the discussion near line 330 of the low oxidation state in the stratosphere. This is surprising, considering the long residence time in the stratosphere and that most of the organic aerosols there came through the upper troposphere, so in order to be less oxidized in the stratosphere they would need to be react, in an oxidizing environment, to reduce the O:C ratio. It is not impossible but surprising and I think unlikely. If true it is important. As correctly cited, Benoit et al. saw the same thing with a similar technique to this manuscript. However, Appel et al. 2022 (cited, but only for sulfate) found the exact opposite result with an aerosol mass spectrometer (AMS). They measured very high O:C ratios in the stratosphere, higher than the troposphere. An “f44” of about 0.28 (Appel et al, Figure 11) corresponds to an O:C atomic ratio greater than 1 (Aiken et al., EST, 2008). There is a similar discrepancy for H:C (Appel et al. and Ng et al., ACP, 2011). The stratospheric Appel et al. data on figure 5 in this manuscript would be almost at the embedded pie charts. Conference presentations of AMS data from the ATom mission agree with Appel et al. (https://espoarchive.nasa.gov/archive/browse/atom/DC8/AMS-60s). Either the AMS is drastically overestimating O:C or the UHPLC/electrospray is drastically underestimating it. Do highly oxidized compounds make it through your column? You don’t have to solve the comparison to AMS in this manuscript, but it should be acknowledged better.

There is some confusion about the Esler et al. reference. It is mostly about high OH concentrations in mixed tropospheric and stratospheric air rather than the concentrations in one or the other. More generally, relative (mixing ratio) OH concentrations are higher in the stratosphere than in the troposphere; absolute (cm-3) concentrations are lower in the stratosphere just because of air density. The diffusion coefficient of OH is higher in the stratosphere than the troposphere, again because of air density. The overall impact on oxidation rate is complex, but the long residence time in the stratosphere implies a lot of opportunity for oxidation.

2) I would like to see a little more discussion of the analytical methods for those with moderate expertise. What would you tell somebody who was an expert in a related field, maybe something like gas-phase atmospheric mass spectrometry, about the strengths and weaknesses of your technique? For example, are there certain classes of compounds where the blanks are significant and other classes where they are insignificant? What classes of compounds might be missed by the ionization method? Another example is my question above about how well highly oxidized compounds make it through the chromatography column. This doesn’t have to have a huge amount of detail, just some major points.

3) Could you add a table or other information on a handful of the most abundant compounds? I agree we don’t want massive lists. But for example, is there one organosulfate (glycolic acid sulfate, IEPOX sulfate, or ?) that is sometimes more abundant, and what it is its concentration? Oxalic acid has been identified as a small but significant (a few %) of aerosol organics in some remote environments. Is it measurable? Maybe a table of the two or three most abundant compounds in each major category (like CHOn, CHOS, not necessarily every category) and how they varied between samples.

4) I found some of the colors on Figure 4 and subsequent figure impossible to associate with the legend. I cannot tell for sure which one is CHOa, CHN, or CHNO. CHOP and CHOS can be distinguished when the bars or slices are big but not when they are small. I’d suggest using hatching on some of the categories to help distinguish them. It would also help if the legend were in the same order as the bars: why is CHN right above CHOn in the bars but at the other side of the legend? Or am I mixing up the colors?

5) Very minor: Line 349 and following “Level 2”, etc. is not defined. Figure 5, please specify atomic or mass O:C.  Line 231 about sulfate versus altitude a better reference would be Wilson et al., 2008, www.atmos-chem-phys.net/8/6617/2008/.  Line 29 the 50% organic fraction only applies just above the tropopause.

Review of “Organic aerosols mixing across the tropopause and its implication for anthropogenic pollution of the UTLS” by Breuninger et al.

General comments

This manuscript presents interesting and valuable datasets on organic aerosol composition in the UTLS, an important and understudied region. The authors describe the collection of UTLS aerosol samples from an aircraft platform and subsequent detailed offline molecular-level analysis. The study is within the scope of ACP and should be of broad interest to the atmospheric science community. However, there are areas where the discussion of chemical composition results could be improved, especially in Section 3.5 (“Non-target analysis of organic compounds within different parts of the UTLS”). More clarity in interpretation would strengthen the manuscript.

A major scientific concern I have is the results and discussions of the oxidation state in Figure 5 and the section “Comparison of chemical characteristics.” It is surprising to me that the stratospheric organic samples appear less oxidized than the tropospheric samples, given the longer aerosol residence times in the stratosphere and the generally oxidizing environment there. Actually, the reported O/C values (< 0.5 for most data) in Figure 5 for both stratospheric and tropospheric samples are also low compared with ambient aerosol summaries (e.g., Chen et al., 2015: https://agupubs.onlinelibrary.wiley.com/doi/10.1002/2015GL063693). This raises the possibility that the offline analysis might be missing more oxygenated, highly polar species.

Have the authors compared the offline O/C and H/C results with online AMS measurements for validation? This would be important, given that AMS data are available for these flights and could reveal whether highly oxidized material is underestimated by the offline approach. The authors should discuss this explicitly, as it has implications for the broader interpretation of UTLS organic aerosol properties.

I also have a few specific questions and comments.

Specific comments:

1. It would be helpful to include additional references on the radiative and chemical importance of UTLS organic aerosols, such as:

• Murphy et al., 2021: https://acp.copernicus.org/articles/21/8915/2021/
• Li et al., 2021: https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2021GL094427
• Solomon et al., 2023: https://www.nature.com/articles/s41586-022-05683-0

1. Line 79-80: Please clarify which aerosol loss processes are included in the sampling efficiency calculation. Does this account for non-isokinetic sampling bias at the inlet tip?
2. For all reported concentrations in µg m⁻³, please state whether they are given at STP or ambient conditions. This is important for comparison with other studies.
3. In the section “CHOS, troposphere vs. stratosphere,” you describe a correlation between organosulfates and sulfate concentrations measured by the online AMS. Could you clarify how the offline method distinguishes organosulfates from inorganic sulfate? In addition, can the online AMS measurements provide any direct information on organosulfates beyond the bulk sulfate concentration?
4. Table 2 and Figure 3: The fraction/trend of CHOS (organosulfates) in the upper troposphere and lower stratosphere appears to be opposite for F05 and F09. Could this be related to differences in tropopause fold influence versus convective injection between the two flights, or are there other possible explanations?
5. Figure 6: The colors for different samples within a single flight are difficult to distinguish, and the stratospheric samples are not easily identifiable. Consider using a more distinct color palette and clearer legends.