SimGlycan® predicts the structure of a glycan using mass spectrometry data. SimGlycan® accepts the experimental MS/MS data generated by a mass spectrometer, matches them with its own database of theoretical fragmentation of over 8,000 glycans and generates a list of probable glycan structures.
Each structure is scored to reflect how closely it matches your experimental data. Other biological information for the probable glycan structures such as the glycan class, reaction, pathway and enzyme are also made available for easy reference.
Glycan & Glycopeptide MS/MS data analysis tool
SimGlycan® is an innovative glycan MS/MS data analysis tool. SimGlycan® predicts the glycan structure, scores it and generates a list of probable glycans that closely match the your experimental MS profile saving you the time and the frustration of laborious work.
Glycan MS/MS Data Analysis of Glycans for Studying Glycosylation
Glycosylation is the result of addition of a glycan to a protein and represents the most common of all the known protein post-translational modifications. Glycans have 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.
For facilitating glycan analysis studies, SimGlycan® predicts the structure of a glycan from the MS/MS data acquired by mass spectrometry. It 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 (the AB SCIEX 4800 Plus MALDI TOF/TOF™ Analyzer, the AB SCIEX 4000 QTRAP® System, and the AB SCIEX QSTAR® Elite System) and Bruker Daltonics (APEX, micrOTOF, micrOTOF-Q and esquire series).
SimGlycan® matches the experimental MS profiles with its own theoretical fragmentation database and generates a list of probable glycan structures. Each structure is scored based on how closely it matches the experimental 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, saving the time needed to retrieve this information from several resources. The predicted glycan structure along with its biological information facilitates the study of glycosylation, which in turn assists glycoprotein characterization.
Features
Robust Glycan Database
The SimGlycan® database is a large relational database populated with theoretical fragments of known glycan structures made up of 62 different monosaccharides. Every glycan in the database is fragmented for each of the possible fifty one reaction conditions using an intensive fragmentation algorithm. This ensures that the probable glycan fragments reported are comprehensive and accurate.
The database is the largest commercial-available glycan database and is hand-curated to ensure the highest fidelity information. SimGlycan® database supports 8184 glycans, 5296 biological sources, 3774 glycan compositions, 5620 classes, 204 biochemical reactions, 150 biochemical pathways, 184 enzymes and 8143 database links.
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 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.
- Glycosidic Fragments: Single glycosidic and glycosidic/glycosidic fragments are displayed.
- Cross ring Fragments: Single cross ring and glycosidic/cross ring fragments are displayed.
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.
Draw Glycans
SimGlycan® enables users to draw and edit glycans and glycopeptides. 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.
A list of glycans along with their scores are displayed in the Search Results Pane. 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
Domon and Costello, (1988),
"A Systematic Nomenclature for carbohydrate fragmentations in FAB-MS/MS Spectra of Glycoconjugates”, Glycoconjugate 5:397-409.
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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.
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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.
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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. |
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