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

2. A High Throughput Lipid Characterization Tool using MS Data2 2

3. Major features
Comprehensive database containing 40, 298 lipids, 1,509,305 structure-specific in-silico MS/MS characteristic ions, and over 5,200 target masses of PIS/NLS
A software tool capable of supporting Shotgun, MALDI-, LC-, MS and MS/MS workflows
Identify lipids for 10,000 MS/MS scans in a batch
Isotope peak correction to facilitate accurate quantitation of lipids
Portable reports in Microsoft excel, HTML, CSV, JPG, PNG files. 3 3

4. SimLipid® DB: You Can Customize4

5. Create a new project
Specify a project name and click “Create” 5 5

6. Import data from native as well as standard data files
Import Shimadzu (.lcd) files 6

7. Shortcut for importing “Shimadzu” data
Browse to the location of Shimadzu files, select the files (multiple selection is possible)
and click “Open” 7 7

8. Selection of scans & specify range for each sample within a file
1.Select a sample within a file
2. Select All Scans of a sample, to
select all the scans in one click
4. Click “Load Scan”

9. Averaged Scans Loaded in Project Management Panel

10. Model Experiment Design for targeted lipid identification
3. Shortcut to Model Experiment Design
2. Analyze > Lipid Quantitation > Model Experiment Design
4. Select only average profiles for experiment design and press “OK”
1. Select the Lipid
Quantitation node 10

11. Model Experiment Design
1. Specify Experiment Name
Specify error tolerance for mapping Target Mass
entered with Target Mass stored in the database
2. Specify Sample Name
5. Click to transfer all the information
into selected profiles table
3. Select a sample
7. Press “OK”
4. Select all scans
Polarity and Target Mass and Scan Type information is read automatically from the file
6. Click on Map Target Mass Database option to
map the target masses with SimLipid's target
fragment database. 11

12. Target Mass Mapping – review the mapped fragments
Results obtained for Target Mass = 241.1 12

13. Target Mass Mapping – review the mapped fragments
Specify error tolerance for performing Exact Mass search with the SimLipid Database. 13

14. Specify peak correction parametres & click “OK” to perform search14

15. A high throughput search ID number is generated
HTP ID 15 15

16. Check HTP Status and Load Results
Load HTP Results
Click this button to check HTP search status 16

17. Check HTP Status and Load Results
Click this button to check HTP search status 17

18. Check HTP Status and Load Results
Load HTP Results 18

19. Result View of PIS/NLS_241.1_Neg
Note that Glycerolipids with PI class is only reported
Experiment name
Sample name
Notice the hierarchy of experiment, sample and and replicates 19

20. Mark Internal Standard
1. Select a lipid to be marked
as internal standard
2. Select Mark/Unmark/Edit
Internal Standard button
3. Specify the amount of Internal Standard 20

21. Align scans in a sample
1. Analyze > Lipid Quantitation > Align Scans in Sample
Select the experiment name from the drop down list
Select the PIS/NLS/Full Scan nodes to be aligned for a sample 21

22. Scans aligned at sample level
Note here the Internal Standard PC (34:2) is aligned from all the scans in the sample 22

23. Generate Comp. x Conc. Report
2. Select the fragment type and lipid abundance option for generating Comp. X Conc. report
3. Select “Heat Map” to generate heatmap
1. Click on “Comp. X Conc. Report” button
4. Select file type
5. Click OK 23

24. Export Results 1. File > Export Results > Project
2. Select file type
3. Click OK 24

25. Results Exported into MS Excel File25

26. Samples Alignment in an Experiment26

27. Align Samples in an Experiment
Use shortcut button to align samples
Analyze > Lipid Quantitation > Align Samples
1. Select the Experiment Name
2. Select the Samples to be aligned
3. Select the alignment options
4. Click OK

28. Lipids Aligned at Sample Level
Lipids aligned from all three samples i.e. Sample 3, 4 & 5 28

29. Quantitation at Experiment Level

30. Quantified lipids at experiment level

31. 31