Robust Glycan and Glycopeptide Database

The SimGlycan® database is a large relational database containing 9560 glycans, 22814 glycoproteins, 5876 glycans with known biological sources, 6231 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.

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, Glycome db, JCGGDB).

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, thereby enhancing the accuracy of the final search result. SimGlycan® allows direct automatic loading of files generated by mass spectrometers from AB SCIEX (TripleTOF™ 5600 System, TOF/TOF 5800, 4800 Plus MALDI TOF/TOF™ Analyzer, 4000 QTRAP® and QSTAR® Elite Systems) 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.

High Throughput Analysis

Rapid advancement in mass spectrometry enables high throughput experimentation for glycan identification. To keep pace with such advancements, SimGlycan® can analyze LC-tandem MS runs containing hundreds of scans in batch mode. Furthermore, users can create and use search parameter templates that can be applied to all data sets.

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 load up to 1500 MS profiles. The projects can be classified on the basis of the source, the lab or the research goal. This is important, especially when conducting large scale glycan analysis projects.

You can access glycan related information at the click of a button. Unlike web based applications, SimGlycan® saves it on your own computer. The available information consists of:

Glycan Structure: Displays the molecular structure (carbohydrate sequence) of the glycan.

Glycan Fragments: Displays the nomenclature, structure, m/z value and mass using Domon Costello rules of fragmentation. A serial number is assigned to each fragment.

i) Glycosidic Fragments: Single glycosidic and glycosidic/glycosidic fragments are displayed.

ii) Cross ring Fragments: Single cross ring and glycosidic/cross ring fragments are displayed.

Glycopeptide Structure: Displays the peptide sequence and the sites of protein glycosylation along with the glycan structures.

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. Read more...

Draw Glycans

SimGlycan® enables users to draw and edit glycan and glycopeptide structures. A monosaccharide, peptide chain or a substituent 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 his modification brings the theoretical glycan closer to the experimental data. This feature greatly assists in resolving glycan structures, especially when data for glycans of interest is not yet available.

Accurate Glycan Ranking

All the possible glycan structures are ranked and scored based on our 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 our database. The glycans with the same mass are then ranked in decreasing order of their intensities (Apte & Meitei, 2009).

A list of glycans along with their scores are displayed in the Search Results Pane, as a result 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® enables you to assign your own rank to predicted structures.

Fragment nomenclature is based on the standard Domon & Costello rules (1988) alongwith the rules described in Cooper et al. (1999)

References

Apte A, Meitei N S, (2009). Bioinformatics in Glycomics: Glycan Characterization with Mass Spectrometric Data Using SimGlycan™. In: Jianjun Li, eds. Functional Glycomics: Methods and Protocols. Volume 600 USA: Humana Press: 269-281.

Domon and Costello, (1988),"A Systematic Nomenclature for carbohydrate fragmentations in FAB-MS/MS Spectra of Glycoconjugates”, Glycoconjugate 5:397-409.

David J. Harvey,"Collision-induced fragmentation of negative ions from N-linked glycans derivatized with 2-aminobenzoic acid ", Journal of Mass Spectrometry, 5: 42-653.

Wuhrer M and Deelder AM,(2006),"Matrix-assisted laser desorption/ionization in-source decay combined with tandem time-of-flight mass spectrometry of permethylated oligosaccharides: targeted characterization of specific parts of the glycan structure", Rapid Commun. Mass Spectrom. 20: 1–9.

Morelle W, SlomiannyMC, Diemer H, Schaeffer C, Dorsselaer AV and Michalski JC, (2004)," Fragmentation characteristics of permethylated oligosaccharides using a matrix-assisted laser desorption/ionization two-stage time-of-flight (TOF/TOF) tandem mass spectrometer", Rapid Commun. Mass Spectrom. 18: 2637–2649.