Comments:

This manuscript systematically validates the capabilities and limitations of PTR-ToF-MS in measuring furanoids, highlighting the need to account for fragmentation and isomeric interferences in biomass burning (BB) research. The findings provide essential data and guidance for improving the accuracy of VOC measurements. The results presented are insightful and are expected to be useful to the PTR-MS and BB communities. While the study presents a novel and valuable research angle, the manuscript's structure (e.g., Methods) requires significant refinement. I recommend its publication to AMT, after the authors have addressed the following comments.

1. For introduction, several issues in structure, clarity, and conciseness need to be addressed to improve readability and scientific communication. My detailed comments are as follows:

1.1  Organization and Logical Flow

The Introduction attempts to cover a broad range of information, but its current structure is overly dense and lacks a clear logical progression. Key ideas are often repeated or presented out of sequence.

1.2  Study Objective and Scope

The study objectives are mentioned twice, in two separate places, with some redundancy. It would be more effective to consolidate this into a single clear statement toward the end of the Introduction. Additionally, the last paragraph should more directly explain how the work addresses the identified gaps.

1.3  Redundancy and Repetition

Several concepts are repeated unnecessarily. For example, the dominant role of biomass burning as a source of furanoids is stated in multiple places with similar wording. Similarly, the discussion of specific furanoids and their atmospheric roles appears both before and after the study objective is introduced. These points should be consolidated for conciseness.

2. For the Methods section, It is recommended to divide the Methods section into several subsections for better clarity and readability. The details of standard gas should be shown here but not in results.

3. The results shown in Figure 2 demonstrate that the fragmentation of certain furanoid species can vary dynamically with changes in E/N. Therefore, readers may also expect to see a plot of fragmentation ratios as a function of E/N.

4. The y-axis in Figures 3 and 4 is labeled in Ncps, which may make it difficult for readers to interpret the relative changes in signal intensity. Using relative signal values—for example, normalizing the maximum to 1—would improve clarity.

5. Can you also provide the relationship of the Reagent ion signals and m39/m21 as a function of water vapor mixing ratios in the instrument? This can help clarify for readers the range of water vapor concentrations corresponding to your humidity experiments.

6. Lines 228-230: “For most species, the mixing ratios in the tank changed by less than 1 % in the seven years since the standard was made (Furanoids summarized in Table 2 with the remaining VOCs in Table A1).” Please clarify the details of how the absolute concentration in the tank was measured for 2017 and 2024, including the measurement methods used.

7. Lines 228-230: “Table A1 shows the same for the other 21 VOCs in our gas standards. For the furanoids reported here, we find that direct calibrations for all furanoids except 5-methylfurfural agree within less than 42 % of those calculated from their molecular properties.” Please provide the k_PTR values used in your sensitivity estimations. It is also recommended to discuss the possible factors that may have contributed to the large discrepancy between the estimated and measured values for 5-methylfurfural.

8. Lines 264-266: “We also find that the correlation between kptr and the measured sensitivities for 25 directly calibrated VOCs decreased by 33 % in the seven years from 2017 to 2024, representative of the overall decrease in instrument sensitivity described above.” The correlation (R) between k_ptr and sensitivity should not change simply because the overall sensitivity decreases. Does 'correlation' in this context refer to the slope between the two variables or the correlation coefficient (R)? If the correlation (R) indeed decreases with a reduction in general sensitivity, please provide further explanation.

9. Lines 295-297: “Similarly, methyl furans at m/z 83.049 and furaldehydes at m/z 97.065 also have a higher unknown fraction in the field measurements. This may be due to the rapid change in smoke composition as it ages post emission, with unidentified isomers or fragments being formed.” Considering that the variability in fragmentation fractions may result from rapid changes in smoke composition, could the authors elaborate on how this might impact measurements in ambient air? Are there any ambient observations (e.g., urban environment but not wildfire) data available to support this? In light of the potential interferences, is furan—or other furanoid species—still a reliable tracer for biomass burning?

Other comments:

1. The reference lists in several sentences are extensive and somewhat overwhelming. In some cases, citations could be streamlined or selected more selectively. Additionally, references should be consistently ordered chronologically, e.g., (Akagi et al., 2011; Stockwell et al., 2015; Koss et al., 2018; Andreae, 2019; etc.).
2. Please unify 2,5-dimethylfuran or 2,5-dimethyl furan.
3. Line 41 Typos for 2-furalehdye
4. Lines 52 “photochemical chemical aging” should be photochemical aging.
5. Table 3 What does 'unknown' refer to in your table? Please clarify its meaning in the text.
6. Line 172 Typos for malic anhydride
7. Lines 324-326 It is recommended to specify whether “higher” refers to concentration, sensitivity, or signal intensity to avoid ambiguity.
8. Line 326 “The full extent of these interferences is currently difficult to quantify“ It can be helpful to state the specific reasons for this difficulty.

Permar et al. present an analysis of PTR-ToF-MS responses to furanoid compounds to address reported uncertainties associated with quantifying furanoids in ambient biomass burning smoke. Furanoids are important VOCs emitted in wildfire smoke that have been well-quantified by PTR-ToF-MS in laboratory settings (e.g., Koss et al. 2018), yet work by Permar et al. 2021 and Gkatzelis et al. 2024 show that field observations of furanoids have large discrepancies relative to GC-MS techniques. This difference could be associated with challenges in PTR-ToF-MS detections of furanoids, detection of previously understudied isomers, or instrument interferences associated with fragmentation. This paper evaluates the PTR-ToF-MS response to furanoids to determine detection robustness.

Overall, the authors show that furanoids are well quantified by PTR-ToF-MS and that detection is not strongly impacted by instrument operating conditions, including relative humidity and E/N. Furthermore, furanoids exhibit remarkable stability in certified calibration standards, implying that long-term monitoring can be achieved by regular instrument calibration.  These results demonstrate that field discrepancies are not likely due to instrument detection issues, but rather to fragmentation interferences or detection of unknown isomers. More work is needed to quantify product ions in ambient smoke using GC-preseparation , or other separation techniques.

The manuscript is well-written and an important contribution towards quantifying a key VOC class emitted from wildfire smoke. I recommend publication and only have minor comments that the authors might consider.

Line 15: This statement might be confused with the stated impact of humidity dependencies at line 12. Perhaps reiterate that this variability in hydrolysis is associated with changes inE/N rather than humidity.

Line 86 – 87: This section is a very nice description of PTR. It would be helpful to include some equations to inform readers who may not be familiar with hydration or C-C fragmentation in PTR-MS.

Line 100-103: This section is a very nice description of PTR. It would be helpful to include some equations to inform readers who may not be familiar with hydration or C-C fragmentation in PTR-MS.

Line 113-117: This is great information. Is ethyl acetate non-fragmenting? Likewise, do any of the isotopes pose any interferences of concern? I think this is useful to note for others who may consider ethyl acetate as a solvent.

Line 181-183: It is also interesting that, in general, you see higher sensitivity at lower E/N (Section 3.2). It is likely that the furanoids are reactive towards the (H2O)H3O+ cluster (similar to some oxygenates, like acetone) and higher E/N results favorable energies that enhance the mechanism noted here. The PA for the water dimer is ~801 kJ/mol (Yuan et al. 2016). The PA for furfural is ~850 kJ /mol (https://pubmed.ncbi.nlm.nih.gov/23147827/). So it's quite possible that furfural (and probably the other oxygenated furanoids) are reacting with the water cluster and resulting in unique product distributions. This should be noted as a possible explanation at lines 213-215.

Table 1: Suggest changing “Fragments” to "Fragments and other products"

Line 261-263: Perhaps some of these differences could be attributed to reactions with the water cluster, as noted above.