Category Proteomics>Mass Spectrometry Analysis/Tools

Abstract SimGlycan® is an innovative tandem mass spectrometry (MS/MS) data analysis tool.

SimGlycan® predicts the glycan structure, scores it and generates a list of probable glycans that closely match the given mass spectrometry (MS) profile. Both glycopeptide and released glycan profiles are supported.

For glycopeptide analysis, SimGlycan® identifies the peptides along with associated glycan structures, using the mass from enzymatically cleaved glycopeptides or precursor ion m/z values.

MS/MS data analysis can be performed for a selected glycopeptide to check its proximity with the experimental data. No information regarding the peptide sequence or peptide mass is needed for this analysis.

Glycan & Glycopeptide MS/MS Data Analysis for Studying Glycosylation -- Protein Glycosylation, which is a key post-translational modification (PTM), is the result of addition of a glycan to a peptide sequence. Glycopeptides are known to exhibit multiple biological functions.

In order to identify distinct functional properties for defined structural features, detailed information on the respective glycan moieties is essential.

Glycans have also been found to participate in many biological processes including embryonic development, inter and intracellular activities, coordination of immune functions, pathogens homing on their host tissues, cell division processes and protein regulations and interactions.

SimGlycan® supports MS/MS profiles of both glycopeptides and released glycans with different chemical derivatives such as permethylation, and various reducing terminal modifications.

These profiles can be uploaded in SimGlycan® using standard file formats or directly from ‘mass spectrometer’ raw file formats from Applied Biosystems (4800 Plus MALDI TOF/TOF™ Analyzer, the 4000 QTRAP® System and the QSTAR® Elite System) and Bruker Daltonics (ultrafleXtreme™ MALDI TOF/TOF, ultraflex™ MALDI TOF/TOF, autoflex™ TOF and TOF/TOF, maXis™ UHR-TOF, micrOTOF™, micrOTOF-Q™, solariX™ Qq-FTMS, and amaZon™ ion trap series).

Other mass spectrometers are supported using mzData and mzXML. No matter what make your instrument is, the output can be converted to these formats using third party tools.

SimGlycan® matches the experimental MS profiles with its own ‘theoretical fragmentation’ database and generates a list of probable candidate glycan structures. Each structure is scored based on how closely it matches the experimental mass spectrometry data.

Additional known biological information for the structures such as glycan class (N-Linked, O-Linked, heparin, lipopolysaccharide, etc.), reaction, pathway and enzyme is displayed. The predicted glycan structure along with its biological information facilitates glycosylation analysis, which in turn assists glycopeptide characterization.

SimGlycan® Additional Features/capabilities --

1) Robust Glycan and Glycopeptide Database - The SimGlycan® database is a large relational database containing 9,560 glycans, 22,814 glycoproteins, 5,876 glycans with known biological sources, 6,231 glycans with known classes, 263 biochemical reactions, 194 biochemical pathways, 250 glycan related enzymes and 9,521 other database links.

The database is continuously updated as information on additional glycans is published.

2) Comprehensive Result Analysis - For every probable glycan structure, SimGlycan® provides glycan fragments, structure, sequence, composition, glycan mass, class, reaction, pathway, enzyme and other database links (CarbBank).

SimGlycan® accepts experimental m/z and intensity values of both released glycans and glycopeptides. It allows you to specify the number of antennae, reducing terminal monosaccharide and non-reducing terminal monosaccharides expected for the structure.

Set the precursor ion error, precursor ion m/z, spectrum peak m/z error, glycan derivatization, ion mode, the adduct and the advanced search parameters such as:

3) Project Management - SimGlycan® provides a comprehensive project management, associating results with input profile and search parameters.

You can open any number of projects. Each project can include up to 10 MS profiles. The projects can be classified on the basis of the source, the lab or the research goal.

You can access glycan related information at the click of a button. The available information consists of:

4) Annotate Mass Spectra and Generate Reports - SimGlycan® can annotate mass spectra using cartoons or Domon-Costello nomenclature. The charge state of the fragment is also depicted.

5) Draw Glycans - SimGlycan® enables users to draw and edit glycan and glycopeptide structures. A monosaccharide, peptide chain or a sub- constituent such as HSO3, ETN can be added or deleted and branching points and ‘anomeric linkages’ can be modified at the click of a button.

At each step, the fragmentation of the drawn structure enables a user to compare the experimental and theoretical data, enabling the user to see whether their modification brings the theoretical glycan closer to the experimental data.

6) Accurate Glycan Ranking - All the possible glycan structures are ranked and scored based on the manufacturer's proprietary search and scoring algorithm.

The ranking algorithm, equipped to handle multi-charged fragment and product ion data, is based on calculating the glycan score, which is a numerical representation of how close the experimental mass of the glycan is to the mass of the glycans included in the manufacturer's database.

The glycans with the same mass are then ranked in decreasing order of their intensities.

A list of glycans, along with their scores is displayed in the ‘Search Results Pane’, as a result of results of glycan analysis. The highest rated ‘glycan sequence’ is displayed at the top of the list.

This glycan represents the most probable glycan structure followed by the rest in decreasing probability. SimGlycan® also enables you to assign your own rank to ‘predicted structures’.

System Requirements

Contact manufacturer.


Manufacturer Web Site SimGlycan

Price Contact manufacturer.

G6G Abstract Number 20551

G6G Manufacturer Number 102176