General Comments:

Pushing down the detection limit of APi-TOFs is a significant advancement in atmospheric measurements and is highly relevant for Atmospheric Measurement Techniques. In this manuscript, the authors demonstrate the use of an ion trap (and an ion funnel) to decelerate and accumulate ions before extraction into the TOF-MS, thereby reducing the detection limit below dozens of molecules cm⁻³.

This is an important technical development that could enable the detection of extremely low-concentration species. The setup makes APi-TOFs measuring after DMA possible, for size-selected chemical composition during atmospheric nucleation processes. Therefore, I recommend publication after the following minor revisions.

Specific/Technical Comments:

1. Page 1, lines 20–21: I recommend changing the unit from ppq to molecules cm⁻³, or showing both, when possible. A major motivation for achieving such low LODs is to probe nucleation events (as authors mentioned), where reporting in molecules cm⁻³ (e.g., 2.5×10⁴ molecules cm⁻³) is more intuitive and widely used than 1 ppq. That said, using ppq occasionally is fine for readers from the gas-phase or trace gas community. I particularly appreciated Figure 2 and line 237, where both units are shown, this is a good practice and should be applied more consistently.
2. Scientific notation and formatting: Please check the formatting of numbers throughout the manuscript:
   • Page 1, line 41: change “10.000” to “10,000” (use a comma for thousands, not a dot)
   • Page 2, line 57: change “10-5%” to correct scientific notation, e.g., “10⁻⁷”
3. Define abbreviations at first use. Several abbreviations are used without definition:
   • Page 2, line 64: Define “Ts” here rather than in line 65.
   • Page 2, line 66: Clarify what “ioniAPi-TOF-MS” means, is this a typo?
   • Page 2, line 98: Define “DC” at first mention.
   • Page 4, line 147: Define “THAB”.
   • Page 5, line 159: Replace the first “TPAI” with “TMAI”, possibly a typo.
4. Page 3, line 108: Remove “Fig. 1” after “Gate 1”, it is redundant.
5. Page 5, lines 165–166: Please rephrase this sentence. The LOD is not typically defined as the signal from a single ion striking the detector. Rather, it is defined as the lowest signal that can be reliably distinguished from noise. Your explanation in Supplementary Section S3 is much clearer and more accurate: “The lowest possible signal that the TOF detector of the APi-TOF-MS can measure is that of a single ion striking the detector (Sₐₒₙ).”
6. Figure 4 and m/z dependence: Figure 4 presents ion transmission for a specific accumulation time (Tₐ). The authors mention extracting ions at three consecutive time points per spectrum to minimize mass bias during accumulation. I wonder whether the trapping efficiency also varies with m/z, for example, low-m/z ions are unstable due to higher kinetic energy or mobility. Could this be dependent on Tₐ as well? Comparing transmission curves for different Tₐ could be insightful and would strengthen the discussion on mass bias.
7. Page 9, line 312: The authors reference results from Density Functional Theory (DFT) calculations, but note that they are not shown. If possible, please provide a reference to these calculations or supplementary material for readers who may wish to explore them further.

The paper elucidated how they carried out the characterization for atmospheric pressure interface time-of-flight mass spectrometer equipped with an octapole ion trap, where detection sensitivity and ion transmissions are well characterized. I suggest we accept this paper after authors could make some description clearer and add more details.

Comments:

1. Line 66: typo? What do you mean by ioniAPi-TOF-MS
2. You should ensure that each abbreviation is defined before it appears for the first time. For example, in line 87, “ESI” is introduced before its meaning is explained, which you explain them in the following section. In Figure 6, the abbreviations “TPAI” and “THAB” are used in the caption, but they are not consistent with those shown in the figure itself.
3. In Table 1, some units are presented alongside the input parameters, while others are placed with the values. Please make the unit placement consistent throughout the table.
4. In general, did you describe what kind of solutions that you made for ESI to generate the ions shown in Table 2? I did not find them. I think it is better to include this information in paper.
5. In line 147, line 256: How did you operate DMS to select single ions with different mass to charge ratio? You only mentioned the parameters to select the THAB monomer, how about others that you listed in Table 1.
6. Line 198 and 200: Water molecules can also have an effect on the binding energies of ion-molecular clusters, which can help to stabilize the ion-molecular clusters. Please have a look at the paper ‘Computational Comparison of Different Reagent Ions in the Chemical Ionization of Oxidized Multifunctional Compounds’.
7. In section 3.2. How did you operate the system to define the transmission? What kind of ions with what mass that you used to define the transmission? Do you mean all the ions that you listed in table 2?
8. Line 315: Is there any reference here?
9. Line 315-319: What would you obtain in mass spectrum if the dimer ions dissociate? If I understand correctly, I would say, it should be one neutral molecule and one ion-molecule cluster. That means it should not be the neutral monomer in your figure 6. For example, the possible combination should be (C12H28N)2I-, (C12H28N)I- and (C7H16N)I- in panel a, but not (C12H28N)2I-, C12H28N and C7H16N. The same case for panel b.