1. Operation manual of AI SIDA

2. 1st layer : initial screen

3. 1st layer : LC-MS(/MS) data loading
(*.mzXML)
Select a *.mzXML data file and press Open below
Open

4. 1st layer : Chromatogram
When a data file is loaded, a total ion chromatogram appears.

5. 1st layer : Chromatogram
There are four options for a chromatogram
Target ion m/z value & tolerance
This option is for a chromatogram which shares a common fragments (max. 5 common fragments)
Total ion chromatogram
Base peak chromatogram
Extracted ion chromatogram
Extracted common ion chromatogram

6. 1st layer : Chromatogram
On the chromatogram, select a peak and click on the peak. Then, a corresponding mass spectrum appears below.

7. 1st layer : Mass spectrum

8. 1st layer : Scan filter
A full mass spectrum or MS/MS spectrum can be chosen. In the case of MS/MS, the retention time and precursor ion information appear.

9. 1st layer : Molecular identification
For the MS/MS spectrum, its ANN-based classification can be made in the 2nd layer upon pressing the ‘Prediction’ button. On the other hand, when the ‘Search’ button is pressed, molecular identification proceed in the 3rd layer.

10. 2nd layer : initial screen

11. 2nd layer : MS2 data loading
Select a file or files and click the ‘Open’ button below.
MS/MS data loading
(*.csv, xls, xlsx files)
Multiple files can be browsed.
Data file format
Open

12. 2nd layer : MS2 spectrum 확인
Multiple files (spectra) can be selected at the same time
MS/MS spectrum
An intensitty threshold can be set.
When the ‘OK’ button is pressed, the corresponding MS/MS spectrum appears

13. 2nd layer : Descriptor 생성
When the ‘Add’ botton is clicked, the
MS/MS spectrum is binned at a 1 m/z interval and digitized. The binned, digitized MS/MS appears in the right ‘Classification’ window (m/z range: ). When the “Add all” button is clicked, all the binned, digitized MS/MS spectra appear in the ‘Classification’ window.

14. 2nd layer : ANN model loading 및 classification
An appropriate ‘ANN Model’ can be called in by pressing this button.
(*.mat)
When the ‘Prediction’ button is pressed, projection of the binned, digitized MS/MS spectrum onto the ANN model proceeds.
ANN classification results show up.

15. 2nd layer : Save results
The ANN model-based classification results can be saved.

16. 3rd layer : initial screen

17. 3rd layer : MS2 data loading
Database loading (*.mat file)
MS/MS data loading
(*.csv, xls, xlsx file)
Excel data input
- Column 1 : m/z
- Column 2 : intensity
- Column 3 : precursor ion의 m/z value
Select a MS/MS data file and press the ‘Open’ button.
Data file format
Open

18. 3rd layer : Intensity threshold 설정
The peaklist for the MS/MS spectrum can be adjusted by setting a different intensity threshold value. The adjusted MS/MS also appears in the right window. The search result is somewhat sensitive to the intensity threshold value.
3rd layer : Intensity threshold 설정

19. 3rd layer : Molecular search
There are three search options: Peak counting scoring, Simple similarity search, and hybrid similarity search.
Search results show up along with its corresponding scores.

20. Structure identification
3rd layer : Search algorithms
MS/MS spectrum
Structure identification
Peak-count scoring
Simple similarity search
Hybrid similarity search
Simple similarity search
Hybrid similarity search
m/z
100
101
102
103
104
105
106
107
108
109 …
Query 50 30
Library 60
pMF= C 𝑆𝑐𝑜𝑟𝑒 𝑇ℎ𝑒 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑓𝑟𝑎𝑔𝑚𝑒𝑛𝑡 𝑖𝑜𝑛𝑠+10
sMF 𝑄,𝐿 =𝐶 ( 𝑖 𝑄 𝑖 × 𝐿 𝑖 )2 𝑖 𝑄 𝑖 × 𝑖 𝐿 𝑖
hMF 𝑄,𝐿, ∆ 𝑚 =sMF(𝑄,𝐻)
* HSS - Blue: original peaks, Red: generated peaks, Gray: shifted peaks

21. 3rd layer : Comparison spectrum 생성
Upper : adjusted MS/MS spectrum (experimental)
Lower: matched database spectrum (library)

22. 3rd layer : Comparison spectrum
Sample spectrum
Comparison spectrum (PCS, SSS)
Comparison spectrum (HSS)
Unknown MS/MS spectrum
Upper: sample spectrum (experimental)
Lower: library spectrum
Upper: sample spectrum (experimental)
Lower: hybrid spectrum (library)

23. 3rd layer : search result, chemical structure viewer