Operation manual of AI SIDA

1st layer : initial screen

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

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

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

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

1st layer : Mass spectrum

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.

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.

2nd layer : initial screen

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

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

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: 50-800). When the “Add all” button is clicked, all the binned, digitized MS/MS spectra appear in the ‘Classification’ window.

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.

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

3rd layer : initial screen

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

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

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.

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

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

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)

3rd layer : search result, chemical structure viewer