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Computer Interpretation of MS Data

Although glycomics resources have not reached the level of proteomics with respect to databases, there are nevertheless many carbohydrate sites that provide databases and other tools for glycomics. Space does not permit a comprehensive coverage of all available resources, but the CFG site http://www. functionalglycomics.org/static/index.shtml contains a wealth of information on databases and tools for predicting glycan composition from masses and for interpreting fragmentation spectra. Links to most major resources can be found on this site. Other resources of interest include GlycoWorkbench

Stable isotope-labeled reagent for the quantification of N-glycans. Red asterisks indicate C and the blue asterisks show N

Figure 3.10 Stable isotope-labeled reagent for the quantification of N-glycans. Red asterisks indicate 13C and the blue asterisks show 15N.

(http://glycomics.ccrc.uga.edu/eurocarb/gwb/home.action) [344], which is a useful tool for drawing glycan structures (both the CFG and Oxford systems are supported), for interpreting fragmentation spectra and for annotating spectra.

SimGlycan (http://www.premierbiosoft.com/glycan/index.html) is a tool for predicting the structures of carbohydrates from MS" data and accepts data directly from various mass spectrometers, and Proteome Systems has a tool, GlycoMod [345] (http://www.expasy.org/tools/glycomod/), for obtaining glycan composition from glycan masses. GlycoSpectrumScan, developed by Deshpande et al. [346], is a tool for assigning potential glycopeptide compositions based on peptide sequences and potential N- or O-glycan compositions, and GlycoPep DB (http://hexose.chem.ku.edu/sugar.php) is an application that uses “smart searching” to find glycopeptides in a database. Only the compositions of previously characterized glycans are used in order to avoid glycopeptides with implausible structures [347]. CASy (http://www.casy.org) is a site that has a database describing the families of structurally related catalytic and carbohydrate-binding modules of enzymes that degrade, modify, or create

glycosidic bonds. UniCarbKB (http://www.unicarbkb.org/) is an online information storage and search platform for glycomics and glycobiology research. It contains UniCarb-DB (http://www.unicarb-db.org/), which is an online LC/MS/MS database that continues that initiated as EuroCarbDB, and GlycoBase (http://glycobase.nibrt.ie/), a database of HPLC data. Cartoonist [348] is a tool for structurally annotating MALDI spectra.

Following the demise of the Complex Carbohydrate Structure Database (CarbBank) in 1997, a number of other initiatives featuring databases have been launched to aid glycomics. Among these is Kyoto Encyclopedia of Genes and Genomes (KEGG) ([349, 350] (http://www.genome.jp/kegg/glycan), which has its own database of carbohydrate structures, including those from the CarbBank database and a database of known biosynthetic pathways. GlycomeDB (http://www.glycome-db.org) is a database that attempts to combine data from earlier databases such as KEGG, CarbBank, and GlycoCT. During the construction of this database, a critical analysis of data in the CarbBank database found that about 35% of the records contain errors, and it was concluded that data contained in that database cannot, therefore, be used and referenced without verification [351]. Lists of databases and other tools for glycobiology have been published in several reviews [352-357].

 
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