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. Workflow for 2-AB labeled Bovine Fetuin N-Glycan analysis
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
New Project creation
Loading Thermo Scientific native .raw file format
LC-MS peak detection and picking
High Throughput glycan identification for the detected peaks
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. Enter a Project Name and press Create
"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.
Multiple data files can also be selected for loading

8. Microsoft .NET Framework version 4.51 or higher is required
"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 load Thermo Scientific .raw file, you will need Microsoft .NET Framework version 4.51 or higher installed on the computer. Press Help to know more.

9. 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.

10. 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 spectra are selected
3. Press Load Scan

11. 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.

12. 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.

13. 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.

14. 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.

15. 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.

16. 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.

17. 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 button

18. 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.

19. Specify Adduct combinations
"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 Select Adduct check box
2. Press Select Adduct button
3. Adduct Identification window appears. Specify the adduct combinations

20. Check Template Name box and specify instrument specific 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 Instrument or Workflow specific peak picking template

21. Else, specify your own set of peak picking parameters
Specify peak picking parameters
"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 Settings for advance parameters

22. Specify advance peak picking parameters 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.

23. Press Preferred List to create a peaklist of your choice
"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. SimGlycan creates 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.

25. 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 button
3. XIC of the selected compound appears

26. 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.

27. 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.

28. Specify the glycan search parameters
"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.

29. 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.

30. Press Filter for setting filters 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.

31. 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. Press Select All
2. Press Add

32. 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 selected
Press Search

33. 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.

34. 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.

35. 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.

36. 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.

37. 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.

38. View Glycan Structure "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 compound specific row
2. Press Glycan Structure button
3. SimGlycan displays the glycan structure

39. View Theoretical fragments
"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 compound specific row
2. Press Glycan Fragments button
3. SimGlycan displays the list of Theoretical fragments

40. Press Annotated Peaklist see matched and unmatched fragments
Blues are matched fragments
Yellow are unmatched fragments
"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. Generate Mass Spectrum for Annotated peaks
"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 Plot Spectrum

42. Specify Plot Type, Fragment details, 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.

43. Successive Fragment Loss plot
"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.

44. Symbolic Representation plot
"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. Domon Costello Nomenclature plot
"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.

46. 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 within Search Results tab
2. Generate Report window appears. Select the parameters to be exported and press Ok

47. 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.

48. Thank You!