Genetic Code

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15-11-2006

CLC bio New Hardware Accelerator

CLCbio have created the ‘CUBE’. A hardware unit which runs Smith Waterman up to 125 times faster than a 3 GHz desktop computer.

Using the Cube instead of BLAST, improves the quality of the data you're working with! read more..
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SimGlycan Features

Robust Glycan Database

The SimGlycan database is a large relational database populated with theoretical fragments of known glycan structures made up of 26 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 7599 glycans, 4751 biological sources, 3039 glycan compositions, 5077 classes, 196 biochemical reactions, 48 biochemical pathways, 177 enzymes and 7285 database links.

Comprehensive Result Analysis

For every probable glycan structure, SimGlycan provides glycan fragments, structure, sequence, composition, glycan mass, precursor ion 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) along with 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.
  • Precursor Ion Mass: Displays the mass 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.

*Note: Any anion or cation that combines with glycan/glycan fragments to form precursor/product ions. The current version of the program supports only H as the adduct for fragmentation. If you work with Li, Na or K adducts, please do write to support@premierbiosoft.com for further help

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.