UniCarb-DB[1] is a structural and mass spectrometric database used in glycomics. UniCarb-DB provides over 1000 LC-MS/MS spectra for N- and O-linked glycans released from glycoproteins that were manually annotated. Each entry contains reference to published work, information about structure, GlyToucan Accession Number, MS/MS fragmentation with complete peak lists, biological contexts and experimental metadata.[2] The database was created by a collaboration between University of Gothenburg and Macquarie University[3][4] and since November 2016 is hosted by Swiss Institute for Bioinformatics. The database is the first to implement the Minimum Information standard MIRAGE (Minimum Information Required About a Glycomics Experiment) for submission of glycomic MS/MS data into the database.[5]
References
edit- ^ "UniCarb-DB". unicarb-db.expasy.org. Retrieved 2016-11-14.
- ^ Lisacek, Frederique; Mariethoz, Julien; Alocci, Davide; Rudd, PaulineM.; Abrahams, JodieL.; Campbell, MatthewP.; Packer, NicolleH.; Ståhle, Jonas; Widmalm, Göran (2017-01-01). "Databases and Associated Tools for Glycomics and Glycoproteomics". In Lauc, Gordan; Wuhrer, Manfred (eds.). High-Throughput Glycomics and Glycoproteomics. Methods in Molecular Biology. Vol. 1503. Springer New York. pp. 235–264. doi:10.1007/978-1-4939-6493-2_18. ISBN 9781493964918. PMID 27743371.
- ^ Campbell, Matthew P.; Nguyen-Khuong, Terry; Hayes, Catherine A.; Flowers, Sarah A.; Alagesan, Kathirvel; Kolarich, Daniel; Packer, Nicolle H.; Karlsson, Niclas G. (2014-01-01). "Validation of the curation pipeline of UniCarb-DB: building a global glycan reference MS/MS repository". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1844 (1 Pt A): 108–116. doi:10.1016/j.bbapap.2013.04.018. ISSN 0006-3002. PMID 23624262.
- ^ Hayes, Catherine A.; Karlsson, Niclas G.; Struwe, Weston B.; Lisacek, Frederique; Rudd, Pauline M.; Packer, Nicolle H.; Campbell, Matthew P. (2011-05-01). "UniCarb-DB: a database resource for glycomic discovery". Bioinformatics. 27 (9): 1343–1344. doi:10.1093/bioinformatics/btr137. ISSN 1367-4811. PMID 21398669.
- ^ Rojas-Macias, Miguel A.; Mariethoz, Julien; Andersson, Peter; Jin, Chunsheng; Venkatakrishnan, Vignesh; Aoki, Nobuyuki P.; Shinmachi, Daisuke; Ashwood, Christopher; Madunic, Katarina (2018-08-27). "e-workflow for recording of glycomic mass spectrometric data in compliance with reporting guidelines". bioRxiv. doi:10.1101/401141.