1. Accelerating Research in Life Sciences
PREMIER Biosoft
Accelerating Research in Life Sciences 1

2. A High Throughput Lipid Characterization Tool using HDMSE Data2

3. Major Features
Database containing 40,298 lipid structures and 15,09,305 structure-specific in-silico MS/MS characteristic ions.
Load raw data from native files (.raw) for HDMSE workflows.
Data processing – peak detection, peak picking – for LC-, SFC- HDMSE workflows. 3

4. Major Features
Visualize raw data, and processed data – TIC, spectra, XIC of detected compound in retention time scale, XIC of compound in Drift Time scale, XICs overlay of precursor ion m/z, and its fragment ions in Drift Time scale.
High throughput lipid structural identification using exact mass, and product ions from HDMSE workflows.
Automated annotation of MS/MS spectra with IDed lipids, and their fragments. 4

5. Create a New Project
1. File > New > Project 5

6. Create a New Project
2. Enter a project name
3. Click Create 6

7. Import Data from Native as well as Standard Data Files
2. Select file type
1. File > Open > Peaklist Data > Waters Data File > Waters (DIA) > HDMSE (.raw) 7

8. Use the Shortcut to Import Waters Native File as Shown Below
1. Select Waters native file shortcut icon 8

9. Use the Shortcut to Import Waters Native File as Shown Below
1. Select Waters native file shortcut icon
2. Select the file(s)
3. Click Open 9

10. Specify Range
1. Select Profile Data
2. Press OK 10

11. Retrieving Selected Scan Number Information11

12. The Selected Files/Scans can be Viewed from the Project Management
Panel Along with Chromatogram and Mass Spectrum
Loaded Data 12

13. The Selected Files/Scans can be Viewed from the Project Management
Panel Along with Chromatogram and Mass Spectrum
Tabular View
Chromatogram view
Loaded data
selected
Select row
Search Results/ Mass Annotation
& Lipid information
are not applicable for DIA data
Spectrum View 13

14. Chromatogram and Mass Spectrum Zoom Options
1. Pinned Chromatogram view 14

15. Chromatogram and Mass Spectrum Zoom Options
2. Select settings for zooming
3. Click OK 15

16. Chromatogram and Mass Spectrum Zoom Options
Selecting Chromatogram area for zoom 16

17. Chromatogram and Mass Spectrum Zoom Options
Pinned Spectrum View 17

18. Chromatogram and Mass Spectrum Zoom Options
2. Select settings for zooming
3. Click OK 18

19. Chromatogram and Mass Spectrum Zoom Options
Selecting Spectrum area for zoom 19

20. Peak Detection and Picking
1. Analyze > DIA Peak Detection > RT + DT
2. Select Profiles
3. Select Template (HDMSe)
4. Select Settings 20

21. Peak Detection and Picking
1. RT Peaks 21

22. Peak Detection and Picking
2. Precursor Ions 22

23. Peak Detection and Picking
3. Product Ions
4. Press OK 23

24. Peak Detection and Picking
5. Select OK 24

25. Peak Detection and Picking25

26. CID's are Detected and Displayed under LC-MS and MS/MS Data Node26

27. High Throughput Lipid Search
1. Go to Analyze > LC-MS Pre-processing > High Throughput Lipid Search
3. Select MS/MS Data option to perform HTP
search only for MS/MS data
2. Specify Range
4. Click OK 27

28. Specify HTP Search Parameters
1. Select profiles
2. Specify Search Parameters
5. Click Search
4. Click OK
3. Specify Filter Lipids 28

29. High Throughput Lipid Search
5. Click OK 29

30. A high throughput search ID number is generated
HTP ID 30

31. Check HTP Status and Load Results
Click this button to check HTP search status 31

32. Check HTP Status and Load Results
HTP search status-Completed 32

33. Check HTP Status and Load Results
Load HTP Results 33

34. Search results are displayed as shown below
Search Results are displayed here 34

35. Lipid MAPS TG standard mix I (D5 labeled)
Species
# C:DB
Neutral Formula
NH4 adduct
NL sn1+NH3
NL sn2+NH3
NL sn3+NH3 Rt
20:5/22:6/20:5
62:16TAG
C65H89D5O6
993.77
674.57
648.57
14.21
20:4/18:2/20:4
58:10TAG
C61H93D5O6
949.80
628.60
652.60
14.99
14:0/16:1/14:0*
44:1TAG
C47H83D5O6
771.72
526.52
500.52
15.08
20:2/18:3/20:2
58:7TAG
C61H99D5O6
955.85
630.65
660.65
15.54
15:0/18:1/15:0
48:1TAG
C51H91D5O6
827.79
568.59
528.59
15.74
17:0/17:1/17:0
51:1TAG
C54H97D5O6
869.83
582.63
584.63
16.15
16:0/18:0/16:0**
50:0TAG
C53H97D5O6
857.83
556.63
16.31
19:0/12:0/19:0**
542.63
640.63
20:0/20:1/20:0
60:1TAG
C63H115D5O6
995.97
666.77
668.77
17.19
*Not specified in the sample mixture but may be present as a contamination.
**Isobaric species.

36. Mass Spectrum Annotation
Sorting by m/z value 36

37. Mass Spectrum Annotation37

38. Mass Spectrum Annotation38

39. Mass Spectrum Annotation39

40. Mass Spectrum Annotation40

41. Mass Spectrum Annotation41

42. Mass Spectrum Annotation42

43. Mass Spectrum Annotation43

44. Mass Spectrum Annotation44

45. Mass Spectrum Annotation45

46. Mass Spectrum Annotation46

47. Mass Spectrum Annotation47

48. Mass Spectrum Annotation48

49. Mass Spectrum Annotation49

50. Mass Spectrum Annotation50

51. Mass Spectrum Annotation51

52. Mass Spectrum Annotation52

53. Mass Spectrum Annotation53

54. Mass Spectrum Annotation54

55. Generate High Throughput Report
2. Select Profiles
1. File > Generate High Throughput Report
3. Click OK
4. Specify MS/MS Search Parameters
5. Specify the sorting options for organizing results in report
6. Specify the lipid information to be exported in report
7. Select output file type
8. Click OK 55

56. Results Exported into MS Excel File56

57. 57