Mr. Cao,

The IDA approach to data-collection is based on a random appearance of the m/z values of the MS ions with respect to the scan time of the measurement over the whole retention time. Therefore, with increasing with the retention time the corresponding set of m/z variables belonging to given MS ion appear randomly over the different spans of the scan time of a measurement.

The DIA approach there is increasing in the m/z values with increasing with the retention time. Therefore, per a concrete span of the scan time of the measurement there appear first the MS ions with lower m/z-values.

I should mention, however, that despite, the operation mode, the quantification of the mass spectrometric data should be based on stochastic method, because of there are fluctuations of both the m/z- and the MS 'intensity' variables.

Simply speaking, the operation mode does not play so significant role in the fluctuations of the values of the MS variables.

In this context, I would like to focus your attention on our most recently developed quantitative approach based on stochastic dynamics for exact (or absolute) treatment of the MS outcome 'intensity' currently available in the literature and worldwide. We (me and my co-author) have developed and written innovative model equations which connect the latter variable with the analyte concentration in solution. The chemometric analysis correlating between our new formulas and the concentration of the analytes in mixture at concentration leves pg.(mL)-1 and ng.(L)-1 show coefficients of linear correlations up to /r/ = 1. The correlative analysis with independent chromatographic data shows /r/ = 0.99997.

I should only mention that according to the currently available classical approaches to quantify MS outcomes the reliability of the analyses is at about 98 %. Please, consider in this context, references [1,2]. The quantitative treatment of the MS variables per different spans of the scan time of the measurements both relating m/z- and MS intensity values of the MS ions has been detailed in chemometric terms.

(Consider the supporting information files, as well.)

[1] Steroids, 164 (2020) 108750

Stochastic dynamic mass spectrometric quantification of steroids in mixture — Part II; Bojidarka Ivanova, Michael Spiteller

[2] B.Ivanova, M. Spiteller, Stochastic dynamic mass spectrometric approach to quantify reserpine in solution, (2020) in press.

Also, within the framework of the same stochastic dynamic theory, we have shown that the introduced by us stochastic dynamic diffusion coefficient (DSD) reflects the exact 3D structure of the analytes as far as it provides information about the energetics of the MS ions: About the free Gibbs energy values. But, as is well-known any 3D molecular structure shows unique free Gibss energy value, which can be predicted quantum chemically exactly, as well. Thus, via our innovative theory and model equations there is obtained mass spectrometrically not only exact quantitative determination of the analytes, but also their exact 3D structural determination. In the latter case, the experimental mass spectrometric data within our theory are correlated with quantum chemically predicted energies of the MS ions with respect to their 3D molecular conformations and electronic structures.

Explicitly, the application of our stochastic dynamic theory to 3D structural analysis has been presented in our recent review-article [3] where we correlate among experimental mass spectrometric data, theoretical quantum chemical data on the 3D molecular conformations, electronic structures and energetics as well as experimental absolute X-ray diffraction analyses.

[3] Reviews in Analytical Chemistry, Band 38: Heft 2 (2019)

A stochastic dynamic mass spectrometric diffusion method and its application to 3D structural analysis of the analytes; Bojidarka Ivanova, Michael Spiteller

Since, as written above our method is completely new and our, own-authored contribution to the quantitative mass spectrometry and its application as absolute method to determine exact 3D molecular and electronic structures of the analytes, if you have any questions regarding the direct application of our formulas to your systems, then do not hesitate to ask them, herein. We shall provide to you a comprehensive guideline step-by-step.