SimGlycan能从质谱分析中获得的数据预测多糖的结构，应用于生物化学的专业软件。SimGlycan预测聚糖的结构，通过由质谱测定法得来的MS/MS数据，更方便于做糖基化和后修饰研究。SimGlycan接受由质谱仪产生得试验性MS文件，将它们同其自己超过7000个聚糖的理论分段比较，并产生可能的聚糖结构清单。每个结构被记分以反应它们如何匹配实验数据。而其他可能的聚糖的生物信息诸如聚糖的种类、反应、反应途径和酶也可以得到。

Accurate Glycan Structure Prediction
SimGlycan predicts the structure of a glycan from the MS/MS data acquired by mass spectrometry, facilitating the study of glycosylation and post translational modifications studies. SimGlycan accepts the experimental MS profiles generated by a mass spectrometer, matches them with its own database of theoretical fragmentation of over 7,000 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 Mass Spectrometry Identification Tool
SimGlycan is an innovative glycan mass fingerprinting 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 Mass Fingerprinting for Studying Glycosylation and Post Translational Modifications
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. Carbohydrates 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 such studies, SimGlycan predicts the structure of a glycan from the MS/MS data acquired by mass spectrometry. SimGlycan accepts the experimental MS profiles generated by a mass spectrometer, matches them with its own theoretical fragmentation database and generates a list of probable glycan structures. Each structure is scored based on how closely it matches your experimental data. Additional known biological information for the structures such as glycan class, reaction, pathway and enzyme is displayed, saving you from having to retrieve it from many sources.


Features

Robust Glycan Database
The SimGlycan database is a large relational database populated with theoretical fragments of known glycan structures made up of 42 different monosaccharides. Every glycan in the database is fragmented for each of the possible thirty four reaction conditions using an intensive fragmentation algorithm. This ensures that the probable glycan fragments reported are comprehensive and accurate.

Every effort has been made while populating this database to make it extremely high quality, enabling reliable data mining for future applications of glycobiology. SimGlycan database supports 8178 glycans, 7526 biological sources, 3498 glycan compositions, 5406 classes, 196 biochemical reactions, 148 biochemical pathways, 177 enzymes and 7234 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 a glycan generated from a mass spectrometer and allows the user to set precursor ion error, precursor ion m/z, spectrum peak m/z error, glycan derivatization, ion mode and the adduct*. Advanced search parameters include:

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.

Accurate Glycan Ranking
All the possible glycan structures are ranked and scored based on our proprietary search and scoring algorithm. The ranking algorithm 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. Fragment nomenclature is based on the standard Domon Costello rules (1988) alongwith the rules described in Cooper et al. (1999)

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.
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.

When you launch the Fragment window, the name of the fragment along with its structure is displayed. The portion in green displays the accepted or active fragment for which the m/z value and mass are calculated and the portion in grey shows inactive or rejected part of the glycan.
Name: Displays the recommended and alternative names of the glycan.
Sequence: Displays the sequence of monosaccharides.
Composition: Displays the monosaccharidic composition.
Glycan Mass: Displays the mass computed from the glycan structure.
Precursor Ion m/z: Displays the m/z ratio computed from the composition.
Class: Displays an incomplete but ongoing classification of glycans.
Reaction: Displays biochemical reactions where the glycan appears as a substrate or a product.
Pathway: Displays biochemical pathway maps containing the participating glycans.
Enzyme: Provides information and EC number of enzymes for which the glycan is a substrate or a product.
Other Database Links: Displays all CarbBank entries with the same glycan structure.
Generate Report: You can create a comprehensive glycan search report for your lab notebook, publication or sharing information with your colleagues. The report includes the glycan characteristics such as the ID, sequence, name, composition, mass, precursor ion m/z, class, reaction, pathway along with a graphical view of the glycan and its possible theoretical fragments.
SimGlycan highlights the m/z values which match those of theoretical fragments. Upon their selection, it plots, annotates, and exports an MS profile in .png format for your lab notebook.
SimGlycan enables you to assign your own rank to predicted structures, add comments and search fragments by their mass, name and m/z values.

References
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.