Robust Glycan and Glycopeptide Database

The SimGlycan® database is a large relational database containing 8553 glycans, 4029 biological sources, 3773 glycan compositions, 5620 glycan classes, 204 biochemical reactions, 150 biochemical pathways, 184 glycan related enzymes and 8142 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).

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. Acceptable file formats include simple text files, .xls files or the standard output file formats such as mzData and mzXML. No matter what make your instrument is, the output can be converted to these formats using third party tools. Other raw file formats such as wiff and t2d generated by mass spectrometers from Applied Biosystems, 4800 Plus MALDI TOF/TOF™ Analyzer, the 4000 QTRAP® System and the QSTAR® Elite System, are directly supported by the program. 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:

• Class: The class of the glycan such as Glycoprotein, Glycolipid, Polysaccharide, Oligosaccharide, Glycoside, Neoglycoconjugate etc. Glycoproteins are further divided into: N-Glycan, O-Glycan, Glycosaminoglycan, GPI anchor and others.
  
  
• Biological Source: The biological source from which the glycan sample was isolated.
  
  
• Pathway: The biochemical pathway in which the glycan participates as a precursor or a metabolite.

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. 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 subconstituent 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 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® 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.