Wei et al. characterize the distribution, seasonality, and speciation of reactive oxidized nitrogen (NOy) in the upper troposphere using measurements from research campaigns and commercial flights and compare them to a global model simulation to test our understanding of NOy sources & chemistry. They analyze the similarities and differences in the NOy speciation in different regions and seasons and identify discrepancies between the observations and the model. This study tackles an important topic since the cycling of oxidized nitrogen in the global troposphere affects tropospheric ozone and OH, and thus climate and tropospheric oxidant levels. The paper is very well-written and the conclusions, for the most part, are well supported by the data and analysis presented.

Here are some points that need to be clarified further:

(1) The UT is defined as 8- 12 km. This is appropriate for the mid-latitudes. but not the tropics. I understand this might be because the DC8 has a ceiling of 12 km, but this should be clarified.

(2) Lines 159-185: The authors use NO₂ calculated from the photochemical steady state instead of the measurements because of interference in the chemiluminescence instrument. The SEAC4RS TD-LIF NO₂ measurements may also be biased high (Silvern et al. 2018, Shah et al. 2023) and this could affect the TD-LIF measurements of the sum of PANs, etc. which are calculated by subtracting the measured NO₂. Is a correction to TD-LIF measurements of these NOy species needed?

(3) One of the paper's conclusions is that GEOS-Chem underestimates MPN during SEAC⁴RS. MPN seems to make up an unexpectedly large fraction of the observed NOy during SEAC⁴RS, and including it in the sum of the NOy species degrades the correlation with the total NOy measurements (Figure 4). This leads me to suspect that the MPN measurements may be biased high. It would be valuable if the authors could dig in a little more to find further support for the MPN measurements, and the conclusion that our understanding of MPN sources is rather poor. They could, for example, look at the ATom data downwind of the southeast US to see if there is a substantial difference between the total NOy and the sum of the NOy species. Do other studies show a significant underestimate of VOCs in GEOS-Chem during SEAC⁴RS?

(4) Lines 54 - 75 I presume nighttime NOy chemistry in the UT is slow enough to be ignored, but it would be good to describe it briefly and state why it is not important, if that is the case.

(5) Lines 365- 372: The paragraph discusses the minor NOy species not included in the analysis, but it does not discuss particulate nitrates (organic & inorganic). Shouldn’t these aerosol species be included in NOy, even if they are minor in the UT?

(6) I suggest that NOy be called “reactive oxidized nitrogen” instead of “reactive nitrogen,” which includes reduced nitrogen (NH3, etc.). And also that in this work NOy does not include N2O.

Wei et al. use different aircraft measurements combined with a global model simulation to characterise upper tropospheric NOy and assess our understanding of the processes governing it. The manuscript is generally well written and easy to follow. The topic is important and timely, affecting for example tropospheric oxidation capacity and ozone formation. 

Below, I have listed certain areas where I would still like to see more detail, followed by a list of minor comments.

1. The comparison between the IAGOS and DC-8 flights. There is a rather large difference in NOy levels between the two, which is explained to result from differences in flight altitudes (lines 241-242). As the comparison of these two flight measurements forms a core part of the manuscript, I would like to see more detailed comparisons here, like altitude profiles of NOy from the two types of measurements. Do they match up?

2. SEAC4RS stands out from the other campaigns in Figs. 4 and 5. These differences are expected to arise from the high contribution of MPN to NOy in that campaign. Especially the poor correlation seen in Fig. 4 leads me to suspect there may be something wrong with these measurements, or then that MPN would not be properly reflected in the NOy measurements. Could you analyse further, whether these MPN measurements are indeed high and correcy, or may there be some interference in them?

3. Altitude definitions: upper troposphere is here defined as 8--12 km in altitude. However, tropopause may be kilometers higher in the tropics: can you justify the choice of altitude range further?

Minor comments:

Abstract, lines 23-24: fractional/percentage values of the over/underestimation would be useful here

Line 54, Fig. 1: can you provide references justifying these are the main species & reactions?

Lines 61-63: add ref for the photolysis vs thermal decomposition

Lines 65-68: add refs

Lines 76-78: add ref

Line 104: add ref

Lines 105-107: mention that the exact definitions for screening will follow

Line 126: would times relative to sunrise and sunset be more appropriate? You screen for jNO2 as well, but this leads to different representation of high- and low latitudes (as mentioned on lines 139-140). I'm not requesting you to redo all the analyses, but preferably comment on if this has an effect on the results

Line 127: full vertical extent. But this does not include full vertical extent, esp. in tropics

Screening criteria: how much data do these criteria exclude? In other words, how typical are the sought-for background conditions?

Lines 135-136: refs for these screening criteria

Line 137: what does approximately zero mean?

Line 149: ref talks about TD-CIMS specifically

Lines 151-153: ref

Line 154: ref for TD-LIF

Eq. 1, also in the text: NO and NO2 should be in square brackets

Line 181: how is HO2 measured?

Line 184, RO2 relatively insignificant: I could not easily find this in the reference. Is it so?

Line 202: are O3, CO and jNO2 also measured on the commercial aircraft?

Line 222: do you mean below-cloud?

Lines 242-243: ref or show data

Fig. 3 b: is panel b needed?

Lines 261-266: would it be easier to read if common measurements were listed, and then campaign-wise which compounds were included?

Lines 294-296: does including the HCN observations improve the agreement?

Section 3.2: includes long and complicated section on inferred concentrations, should this rather be in the methods section?

Line 359: coincidence of the individual to total NOy? What about disregarding ALKN as they make a relatively small fraction of NOy to achieve higher southern hemisphere coverage?

Lines 366-368: ref for negligible contribution

Line 370: check the reference. For 100 ppt NO the lifetime is 15 seconds, so for the max average NO campaign (SEAC4RS) it is close to a minute. Noontime clear sky photolysis lifetime is around 6 s, longer off-noon and at high latitudes. Not saying that NO3 would be significant, but that people often underestimate NO3 daytime lifetimes

Lines 371-372: how much shorter?

Lines 391-392: ref, or is this your result?

Line 417: ref

Lines 460-461: was this mentioned in the results section?

Line 490: maybe cite all sources here again.