1. Accelerating Research in Life Sciences
PREMIER Biosoft
Accelerating Research in Life Sciences
SimGlycan®  accepts experimental MS/MS data
and compares it with the in silico fragmentation of
known glycan structures present in SimGlycan®
database. This generates a list of known glycan
structures whose fragment mass fingerprint data
is similar to the experimental data. Finally the
possible glycan structures are ranked based on a
proprietary ranking scheme. Biological information
such as class, reaction, pathway, enzyme is also
provided for probable glycan structures that are
useful for the next level of biological research
after structure elucidation studies.

2. Dual Reaction for Analytical Glycomics (DRAG) workflow
SimGlycan®  accepts experimental MS/MS data
and compares it with the in silico fragmentation of
known glycan structures present in SimGlycan®
database. This generates a list of known glycan
structures whose fragment mass fingerprint data
is similar to the experimental data. Finally the
possible glycan structures are ranked based on a
proprietary ranking scheme. Biological information
such as class, reaction, pathway, enzyme is also
provided for probable glycan structures that are
useful for the next level of biological research
after structure elucidation studies.

3. Loading Thermo Scientific native .raw file format
Topics to be explained
Creating a new project
Loading Thermo Scientific native .raw file format
LC-MS peak detection and picking
Isotope labeling and high Throughput glycan search parameter settings
Portable report generation
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

4. Launch SimGlycan and create a new project
To create a new project, go to: File> New Project
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

5. A new project named DRAG appears
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

6. Import Thermo Scientific .raw data file
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
To import Thermo Scientific .raw file, go to: File> Open> MS/MS Data File> Thermo Scientific Data File

7. Navigate SimGlycan to the file location, select the file(s) and press Open
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

8. Load Scan window appears listing all MS and MS/MS spectra
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

9. To load all scans, press Select All
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Press Select All
2. All scans are selected for loading
3. Press Load Scan

10. Press Specify Range to selectively load the spectra
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

11. Upon pressing Load Scan, data loading starts
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

12. Once completed, loaded data file appears under Profile node
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

13. Click on LC-MS and MS/MS Data node
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

14. Initiate LC-MS peak Detection
To initiate LC-MS peak detection, go to: Analyze> LC-MS & MS/NS Data Pre-processing> Peak Detection and Picking
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

15. Peak Detection and Picking window appears
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

16. Select the Data file for peak picking
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Select the data file
2. Press the right arrow

17. Data file is now available under Selected Profile column
Data File is available under Selected Profile column
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

18. Select DRAG LC-MS as the peak picking template
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Tick the check box Template Name
2. Specify the template named DRAG LC-MS

19. Optimized set of Peak picking parameters are automatically selected
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

20. SimGlycan is creating the peaklist
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

21. SimGlycan displays the detected peaks within Peaklist tab
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

22. Press View Chromatogram to view the XIC of a compound
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Click on the compound specific row
2. Press View Chromatogram
3. XIC of the selected compound appears

23. Initiate High Throughput glycan search
To initiate high throughput glycan search, go to: Analyze> LC-MS & MS/MS Data Pre-processing> High Throughput Glycan Search> Released Glycan and Glycopeptide Analysis
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

24. Specify the Peaklist and press OK
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

25. Specify the glycan search parameters, reducing end modification
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

26. Specify Methylamidation as Additional modification
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Check the box Additional
2. Select Methylamidation from the drop down

27. Specify the Isotope labeling method
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Press Isotopic Modification
2. Isotopic Labeling Method window appears

28. Specify the Isotope labeling method
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Select Choose Labeling Method
2. Select 2-AA C12C13

29. Specify the Isotope labeling method
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Isotope's Tag name and Mass shifts are tabulated
2. Check Lock Settings
3. Press OK

30. Specify Modifications on monosaccharide residues
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Check Modified Carbohydrate Residue
2. Press Modification Details

31. Specify Modifications on monosaccharide residues
1. Specify Monosaccharide residues and the corresponding modifications
2. Check Lock Modification
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
3. Press OK

32. Specify Modification Type (Fixed or Variable)
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

33. Press Fragmentation Pattern
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
Press OK

34. Specify Filter to reduce false positives
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

35. Select MS/MS spectra for glycan search
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Select Select All
2. Press Add

36. MS/MS spectra are selected for glycan search
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
MS/MS spectra added
Press Search

37. SimGlycan assigns an High Throughput Search ID. Press OK
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

38. Check Search Status "Draw Glycan" module enables users to :
To check the search status, go to: View> HTP/GpQA Search Status
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

39. SimGlycan displays the search status
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

40. Retrieve the search results
To retrieve the search results, go to: View> Fetch High Throughput Results> Load HTP Request
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

41. Identified glycan are listed within Search Results tab
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

42. Same glycan is identified for both light (12C) and Heavy (13C) labeled samples
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
The glycan with composition: (Gal)2 (GlcNAc)4 (Man)3 (NeuAc)2 is identified for both Light (Tag Name: C12) and Heavy (Tag Name: C13) samples with retention time minute and minute respectively

43. Generate an Excel report of identified glycans
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.
1. Press Generate Report
2. Generate Report window appears. Specify the glycan details to be exported and press OK
3. Press OK

44. Identified glycans, along with their structures are exported
"Draw Glycan" module enables users to :
(1) Draw and edit glycans or glycopeptides structure and compare against experimental MS/MS data.
(2) Check whether the edited theoretical glycan is closer to the experimental one.
Robust Database:
The SimGlycan® database is a large relational database containing 22,456 glycans, glycoproteins, 11,438 glycans with known biological sources, 11,918 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9521 other database links. The database is continuously updated as information on additional glycans is published.
SimGlycan Enterprise Edition enables:
(1) Searching of glycans and glycopeptides against private custom databases.
(2) Creation of sub-databases to narrow down the search.
(3) Users to perform search without internet connection.

45. Thank You!