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Glycan Mass Spectral DataBase (GMDB)

 

Significance of GMDB

Glycomics has lagged far behind proteomics because of analytical difficulties arising from the structural complexity of glycans, such as variations in branching, linkage and stereo-chemistry.  Recently, tandem mass spectrometry has revealed that different glycan structures show their own fragment patterns in their collision-induced dissociation (CID) spectra. We are constructing a multistage tandem mass spectral database using a variety of structurally defined glycans, some of which were prepared using glycosyltransferases in vitro. This database offers a novel tool for glycomics research as it enables users to identify glycans very easily and quickly by spectral matching.

 

Present Status of GMDB

GMDB currently stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans. O-Linked glycans were converted to the corresponding alditols before MS acquisition. The other types of glycan stored in GMDB are mostly tagged with 2-aminopyridine (PA) which can be used for fluorescence detection in HPLC. MSn spectra of glycans containing sialic acids were acquired after methylesterification of sialic acid moieties. All spectra were obtained in the positive ion mode using a MALDI-QIT-TOF mass spectrometer.

 

Future Perspectives

GMDB will be updated on an irregular basis to provide spectral images for a wide variety of glycans including sulfated and lactonized glycans. MSn spectra of the sulfated glycans will be acquired in the negative ion mode as well as positive ion mode. MSn spectra of permethylated and pyridyl aminated glycans will also be fed to GMDB.

 

Acknowledgement

The spectral acquisitions are originally supported by the New Energy and Industrial Technology Development Organization (NEDO).
The construction of this database is supported by Ministry of Education, Culture, Sports, Science and Technology(MEXT).
The network security and Web Application Security are supported by Tsukuba Advanced Computing Center(TACC), AIST.

 

Disclaimer

Research Center for Medical Glycoscience at AIST does not warrant or assure any legal liability or responsibility for the accuracy, completeness, or usefulness of any information available from this website.