## 4 Discussion  
The core of the pseudo-MS/MS spectrum deconvolution method is to reconstruct the correspondence between the precursor and the fragment ions by calculating the similarity of the chromatograms between the precursor and its fragment ions. However, the number of peaks in the chromatogram comparison process is large, resulting in a huge amount of calculation, and the DIA data have a large number of isotope peak clusters, which will bring repeatability to the results. Based on these problems, we proposed CorrDIA, which takes the MS/MS spectrum as the center to process the mass spectra one by one and uses the isolation window information of each MS/MS spectrum to narrow the search space. CorrDIA also removes isotopic peak clusters from each precursor ion mass spectrum and carries out an overall search to remove redundancy in each selection of candidate precursor ions. CorrDIA reconstructs the corresponding relationship between the precursor and its fragment ions, reducing the complexity and difficulty of spectrum analysis.  
We compared CorrDIA with the DIA-Umpire. Our experiments show that both the number of identified peptides and the resolution rate of the spectrum improved. In addition, CorrDIA could also solve the redundancy problem caused by isotopic peak clusters and reduce the redundancy of the same peptide.  
However, CorrDIA was unable to analyze peptides without a precursor ion signal. In addition, due to the ion interference, ion suppression, and spectrum split algorithm of the MS/MS spectra, the number of MS/MS spectra obtained by the pseudo-MS/MS method was relatively small, resulting in a lower identification number than the mass spectra library [23] search method. With the development of mass spectrometry instruments, a correspondence between precursor and fragment ions could be regained by the acquisition of new dimensional information. The ion mobility acquisition technology and the latest sliding quadrupole technology were introduced, and the additional dimensions of collected information were developed into 4D-DIA data acquisition methods as a supplement to the traditional 3D-DIA, which only contains mass-to-charge ratios, strengths, and retention times. 4D-DIA methods, such as DIA-PASEF [17] and Scanning SWATH [16], reconstruct the relationship between mother ions and fragment ions in the secondary spectrum to a certain extent by recording additional ion mobility and four-stage rod dimensional master-ion information, and further improve the data resolution. In the future, the MS/MS spectra-splitting ability could be improved by combining it with deep learning algorithms to identify the high-dimensional characterization of the mother ion and fragment ion chromatograms and by using the higher selectivity of the precursor provided by the 4D-DIA data.  
Methodology, X.Z.; Investigation, R.W.; Writing--original draft, X.Z.; Writing--review & editing, X.Z.; Supervision, Z.Q. All authors have read and agreed to the published version of the manuscript.  
This research was funded by Youth Innovation Team Development Plan of Shandong Province Higher Education grant number 2019 KJN048.  
Not applicable.  
The raw data mentioned in this study can be downloaded from the ProteomeXchange with the accession number PXD005573. The MS/MS spectra of the hela and human data sets were searched against the UniProt hela database (released in August 2022, 459 protein entries) and the UniProt human database (released in September 2022, 20,398 protein entries), respectively.  
The authors declare no conflict of interest.  
CorrDIA is implemented in Python. The source code is provided on GitHub ([[https://github.com/zx/CorrDIA](https://github.com/zx/CorrDIA)]([https://github.com/zx/CorrDIA](https://github.com/zx/CorrDIA))).