This manuscript presents eddy covariance flux measurements of VOCs over a wheat field in Europe with a PTR-Qi-TOF-MS. It identified several most emitted and deposited VOCs for a crop field, and presented their fluxes. The paper is a bit hard to follow. But studies for reactive species over croplands are rare. I still consider the paper provides valuable data to the community. The error characterization of eddy-covariance flux calculation is potentially helpful though they are mostly presented in the supplement. I have the following concerns and suggestions:

Main concerns: 

- Abstract: consider shortening it by cutting those introductions (1/3 of the current abstract) and highlight results.

- Sections 2.2.4 and 2.2.5 for Kinetic concentration and calibration: If I understand correctly, this study calibrated 5 VOCs, and the rest VOCs were estimated using the kinetic approach (Eqn. 1). This is a critical component of the paper, but unfortunately, it is confusing and lacks key details and discussions on measurement uncertainty. The kinetic approach using the same rate constant for all VOCs is subject to large uncertainties (maybe as high as +/-200% or more). Uncertainty and how that affects conclusions of the work should be discussed. What is the uncertainty for calibrated VOCs? How frequent was the calibration (what is ‘several time’ as mentioned)? How do these calibrations compare to each other? How do their calibration factors compare to if using the kinetic approach? This should give some range of error estimates, at least for these selected VOCs.

- Many figures in the texts are either not discussed or only very briefly discussed. Consider removing some of them as the manuscript is very long, and key messages would get lost with so much information blended in without actual contribution to the discussion.

- The figures and texts keep changing between using exact mass and species names. It needs to be consistent to improve the readability of the paper. I suggest using species names with exact masses in brackets if the mass is considered important.

- Time series figures are interesting, but it took a while to figure out what they are and how to interpret them. I’d suggest either improving the presentation or captions to explain them.

- Section 3.2 VOC mixing ratio: it doesn’t add much value, and the time series figure 6 is misleading to some extent (see above).

- Figure 9: the deposition fluxes peaked around 5pm local time, which was explained as corresponding to afternoon rush hour. How is that possible since these are flux measurements which reflect a very small footprint given the height of the tower. Are there any traffics within the footprint? Further discussion on the footprint is needed. Later it presents the influence of the farm, and that should also be tied to the footprint discussion.

- Table S2: I cannot find this table in the supplement. It states, ‘See file Loubet-COV3ER-wheat-2016-EC-Supp.Mat-VF.’, but this table of VOC tentative identification is not available. Is the ‘Loubet-COV3ER-wheat-2016-EC-synthesis-fluxes-VF’ what you referred to?

- Section 4.2: Methanol. It is interesting that the study found that its emission increases towards senescence. Several studies have reported that methanol emission peaks when leaves are young during the early growing season, i.e., in the US (Karl et al., 2003; Hu et al., 2011), northern mid-latitude ecosystems (Wells et al., 2012), in MEGAN emission model (Guenther et al., 2012). Does this study suggest different mechanisms for crops/wheat to emit methanol compared to other ecosystems? 

- Sections 4.2 and 4.3. Most of this section read like a literature review, and there is not much new knowledge added from what we already know about biogenic VOC emissions. I’d consider shortening them or likely merging with the previous sections when discussing their mixing ratio/flux results (Sections 3.3, 3.4, and 3.5.)

- Species ‘tentatively attributed to’: This term is overused in the paper. Sure, some compound identifications are tentative, but many others are certainly based on literature and the correlation analysis. A thorough and careful assessment of species identification is needed to address what is tentatively attributed.   

- Section 4.4: influence by the farm. Would the farm affect the flux measurements? Does the flux footprint cover the farm? It should be easy to quantify that influence since footprint analysis is already done.

- Correlation analysis is helpful to identify possible fragmentation. The paper provides the results for two electric fields E/N 130 and 150. Do those excluded species show similar patterns under different E/N fields? Or do they fragmentation patterns change, at least for some masses?

- There are many typos, minor grammatical errors, citation errors. Thorough proofreading could help.

Specific comments: 

- Line 125: What is the purpose of the 16-way sulfinert coated valve?

- Line 144: What is teflonised pump? Explain it?

- Section 2.2.1: what is the mass resolving power of this instrument? It’d be important for species identification.

- Line 158: Lower the electric field to diminish cluster formation and fragmentation. Even 129 Td, there’d be lots of fragmentation. I’d reword it.

- Line 206: Why ‘a single calibration factor for all VOC using toluene’? I thought you performed calibrations for 5 VOCs, no?

- Line 354 and Figure 5: the flux footprint is presented as unitless. It needs to define what the footprint is and how to interpret it.

- Line 798: The sentence does not seem to be complete after ‘New developments in this field would be helpful’?

Reference:

Karl, T., Guenther, A., Spirig, C., Hansel, A., and Fall, R. (2003), Seasonal variation of biogenic VOC emissions above a mixed hardwood forest in northern Michigan, Geophys. Res. Lett., 30, 2186, doi:10.1029/2003GL018432, 23.

Hu, L., Millet, D. B., Mohr, M. J., Wells, K. C., Griffis, T. J., and Helmig, D.: Sources and seasonality of atmospheric methanol based on tall tower measurements in the US Upper Midwest, Atmos. Chem. Phys., 11, 11145–11156, https://doi.org/10.5194/acp-11-11145-2011, 2011.

Wells, K. C., Millet, D. B., Hu, L., Cady-Pereira, K. E., Xiao, Y., Shephard, M. W., Clerbaux, C. L., Clarisse, L., Coheur, P.-F., Apel, E. C., de Gouw, J., Warneke, C., Singh, H. B., Goldstein, A. H., and Sive, B. C.: Tropospheric methanol observations from space: retrieval evaluation and constraints on the seasonality of biogenic emissions, Atmos. Chem. Phys., 12, 5897–5912, https://doi.org/10.5194/acp-12-5897-2012, 2012.

Guenther, A. B., Jiang, X., Heald, C. L., Sakulyanontvittaya, T., Duhl, T., Emmons, L. K., and Wang, X.: The Model of Emissions of Gases and Aerosols from Nature version 2.1 (MEGAN2.1): an extended and updated framework for modeling biogenic emissions, Geosci. Model Dev., 5, 1471–1492, https://doi.org/10.5194/gmd-5-1471-2012, 2012.

The authors present multi-week measurements of hundreds of VOC fluxes over a wheat field. They discuss the technical aspects of their measurement well, making this work quite useful for further investigations. They highlight the highest positive and negative flux compounds, and do a good job expounding upon their significance. Overall, I consider this paper valuable to the community. I have some concerns, listed below. Most importantly, please ensure that the compound assignments are correct and match the very impressive SI. Secondly, while the authors go into significant technical detail, there are still areas to improve clarity, and ensure future studies can benefit from the techniques used in this work.

Abstract: please state the start date and duration of the study in the abstract.

Mass 93.037 or 93.033? In the abstract and at line 802 this mass is referred to as mass 93.037, not 93.033. This is quite important: if the measured mass was 93.037, it may be more appropriately identified as C3H9OS+, or 2-Methylmercaptoethanol as identified in the GLOVOCS database. Additionally, this would put the assigned formula of C6H5O+ some 38 ppm from the measured mass, an error much larger than one expects from the authors’ instrument.

Methods: Please explicitly state the number of days the experiment lasted.

Also, for the sake of our backwards American counterparts, please consider using an unambiguous date format in the text, such as June 3^rd 2016 rather than 03/06/2016 (although the latter is perfectly fine in figures and tables).

Would it be possible to add the events discussed in lines 101-111 to Figure 3?

Section 2.2.1: Can you provide the Reynolds number for the sampling line? Can you comment on the height of the tower, as it seems short relative to the height of the wheat. Does this make calculating a footprint difficult? Also please report the size of the footprint in this section.

Section 2.2.4: This section feels a bit rushed, and as this is an AMT paper it would be appropriate to walk the reader through these steps. Additionally, along with section 2.2.5 this would be a good place to discuss uncertainty in both mixing ratio and flux measurements. While many have used the default reaction rate constant to calculate transmission based mixing ratios, the method does have a substantial error stemming from the variability in rate constants. Regarding section 2.2.5, it seems the authors take the mixing ratio calculated in equation 1 and then correct it with a calibration factor derived from the instrument response to toluene. What exactly does this calibration correct for, and why are the mixing ratios calculated using the default reaction rate constant of 2.5e-9  in need of correction, as they are already normalized to the primary ion signal, accounting for MCP and other changes?

In the methods section, please report the amount of time for which you were able to calculate fluxes. For times when you could not, did you do any gap-filling, and if so what was your method.

Results:

For figures 4, 5, 6, 7, 8, the standard deviation ribbons disappear in the final weeks of the plots. Why is this? Also, please add the assigned formula or compounds to the plots, not all of us know that m59.049 is acetone.

Line 366: “The most concentrated VOC at the site were methanol, acetone, C6H4O, propanoic acid, ketene, propyne, acetaldehyde, formaldehyde, and hydrazine acetate (Table S2)” This does not align with the data in table S2. For instance, hydrazine acetate is not listed. Please correct.

In line 485, the authors mention butene (m/z 57.070), but it does not appear in table S2. Please ensure that Table S2 and the main text are in agreement on both names, formulas, and masses. If a compound is discussed in the main text, I would like to see it included in S2. Additionally, have the authors considered that butanol will likely fragment onto the butene assigned ion?

The authors present a measurement of formaldehyde, which shows a high humidity dependance in PTR due it having a similar proton affinity as water. Can the authors show some figures in the SI that show their formaldehyde measurement is not too influenced by water vapor concentration? Otherwise I would not report the value, as it is not too discussed and there are many other interesting findings.

Section 3.5: Very interesting!

Discussion:

Large emissions of MeOH have been seen from dairy operations. Could methanol be coming from runoff from the nearby animals?

Table 1: please explain the format of the flux better. I am a bit confused by the table note “Mean ± se [5 – 95 percentiles] and max – min” and how it relates to the fluxes. Also, when using the tilde, “~”, you seem to omit the negative sign, which could lead to confusion. For instance, the first flux column for monoterpenes is negative, but the second reads positive.

Is it possible that the signal at 68.06 is from O2+ ionization of isoprene? If so were O2+ levels stable?

Lines 621-637: This is very good analysis.

4-OPA is missing from Figure 10, please include it. 4-OPA is a known ozonolysis product of squalene a component of human skin oil, and sometimes cited as a tracer for skin oil ozonolysis. It is very interesting to see it emitted/deposited in a wheat field. Is it known if wheat produces squalene as well? Did the authors see a pattern with 4-OPA and ozone?

Figure 11: consider adding the direction of the farm to these plots.

Minor issues:

Line 29: “outmost”?

Line 95: “the field is at around…” remove “at”

Line 93: “The site that is part of a dairy farm receives a lot of nitrogen as mineral or organic matter, which leads to large ammonia emissions” Are you referring to manure and runoff?

Equation 1: are there units for this constant?

Line 223: While I like the idea of a perfect gas constant, I believe you mean “ideal”

Line 288: “7 NL per min” I’m unfamiliar with “NL”

Line 387: “Region” to “region”

Line 467-68: please rephrase

Line 564: extra “.”

Line 673: “leaves” to “leaf”6

Line 682: “under brackets” to “in brackets”

Line 792: “less” to “fewer”