This manuscript utilized an improved source apportionment approach that has been developed recently, binPMF, to deconvolve nitrate CI-APi-TOF mass spectra from a highly-developed, densely-populated urban region in eastern China. The authors identified factors from different sources and discussed the influence of anthropogenic and biogenic emissions. Overall, the manuscript is well written and scientifically interesting. I recommend publication after the following comments are addressed.

1. All figures have a poor resolution. Formatting issues? Please update.
2. Equation 1: Can the authors provide more details about calibration factor determination? Are the inlet configuration and flow rate in the reference the same as these used in this work? Moreover, the reagent ion can have different sensitivities towards different compounds, and the sensitivities also vary for ions from the same species but charged in different ways. Can the authors validate the use of H2SO4-based calibration factor for all species and elaborate more about the potential impact on the results?
3. Equation (2): Can the authors include more details of the equation, i.e. how CS is calculated, k_OH+SO2 value (or calculation) and source?
4. Line 212: “the raw spectra with were…” Some words seemed missing here.
5. Figure 1: Can the authors add the diurnal patterns of all parameters? The NO, temperature, and J(O¹D) diurnals were included in Figure 4 and 12, but it would be good to have a summary plot.
6. Table 1: As mentioned before, the authors may need to consider the effects of assuming a constant ionization efficiency. How credible are the reported concentrations? Can the authors include uncertainties?
7. Line 341: The authors used “autoxidation” instead of “auto-oxidation” elsewhere. Please be consistent. Moreover, the diurnal pattern of Aro-OOMs almost followed that of NO, would autoxidation be suppressed?
8. Figure 8: One obvious difference between the two isoprene oxidation products from this figure is that C5H10O8N2 was mostly attributed to Isop-OOMs and Photo-related factors, while C5H9O10N3 was to Isop-OOMs and Ox & SOA-related factors. As the authors proposed that C5H9O10N3 was more likely to be transported than C5H10O8N2, does this imply that the Ox & SOA-related factor was transported?

This paper discussed the measurements of oxygenated organic molecules (OOMs) performed in Nanjing in eastern China. A nitrate-ion-based chemical ionization mass spectrometer was used to perform these ambient measurements, and source apportionment analysis was performed using a recently developed approach positive matrix factorization on binned mass spectra (binPMF). The authors reported several factors related to anthropogenic VOCs daytime chemistry and biogenic VOCs (BVOCs) chemistry, and they discussed the influences of anthropogenic and biogenic emissions on the formation and evolution of these factors. In general, the manuscript was very well-written and the results were presented in a very clear, coherent manner. The topic is of interest to the atmospheric community. I recommend publication after the authors have addressed the following comments:

1. More details need to be provided for the quantification of OOMs (equation 1) especially since OOMs are the focus of this paper. How was equation 1 derived?
2. Why did the authors assume that the detected OOMs have the same ionization efficiencies as sulfuric acid? Have they tested their assumption? What are the uncertainties that arise from using this assumption?
3. The authors stated that VOCs were measured using a PTR-MS. Was the data used in this paper? It was not clear to me whether and/or how the data was used to support results discussed in this paper.
4. More details need to be provided for equation 2. How was CS calculated?
5. Were calibrations performed during the field campaign? If no, how confident are the authors that the ionization efficiencies for their nitrate-ion-based CIMS source were constant throughout the entire sampling period?
6. Higher resolution figures are needed.