1. EUROCarbDB CCRC – Database for high quality mass spectrometry data Khalifeh Al Jadda 1, Haseeb Yousef 1, Kitae Myong 1, Srikalyan Swayampakula 1, David Damerell 2, René Ranzinger 1, William York 1 1 Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA 2 Imperial College London, London, UK Introduction The establishment of high-quality collection of reference data for mass spectrometric (MS) analysis is a key task required to improve the efficiency and accuracy of glycomics analysis. A library of high quality annotation and reference spectra will not only enable future annotation procedures but also shed light on gas-phase fragmentation mechanisms and the influence device-dependent factors on fragmentation patterns. The need for a collection of standard reference data was identified as a high priority at the CFG workshop on Analytical and Bioinformatic Glycomics in April 2009, and two CFG bridging grants were established to systematically record the MS and MSn spectra of the currently available synthetic N-glycans and O-glycans to seed a high quality reference library. The EUROCarbDB design study has established the foundation for database and bioinformatics tools in the realm of glycobiology and glycomics, into which all interested research groups can feed their primary data [1]. In collaboration with the developers of the EUROCarbDB database, we extended EUROCarbDB to record high quality mass spectrometry data and installed a new instance (EUROCarbDBCCRC) at the Complex Carbohydrate Research Center (Athens, Georgia, USA). Together with members of the bridging grant projects we defined a data submission workflow using MS standard data files (mzXML) and GlycoWorkbench [2] annotation files to submit the spectra and annotation to our database. Summary  The web based mzXML file upload enables users to store experimental MS data in the EUROCarbDB database generated by any mass spectrometer.  Annotated MS spectra can be uploaded by using GlycoWorkbench annotation and data files  Uploaded carbohydrate structures are automatically cross referenced with existing carbohydrate databases by using GlycomeDB cross references. Outlook  A new EUROCarbDB instance will be installed at the Complex Carbohydrate Research Center  Using the implemented upload workflow MS data from standard glycans will be used to populate the database  After population this database can be used as a reference database for MS data and for the development of fragmentation rules which can assist further MS annotation References and Acknowledgements 1.http://www.eurocarbdb.org 2.Ceroni A, Maass K, Geyer H, Geyer R, Dell A and Haslam SM: GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. J Proteome Res, 7(4):1650 – 1659, Apr 2008. 3. Frank M, Schloissnig S: Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci. 2010 Aug;67(16):2749-72. Epub 2010 Apr 4. (and references herein) GlycoWorkbench: (Semi-) Automatic Peak Annotation Figure1: GlycoWorkbench main Interface GlycoWorkbench is a suite of software tools designed for rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data. The graphical interface of GlycoWorkbench provides an environment in which structure models can be rapidly assembled, their mass computed, their fragments automatically matched with MSn data and the results compared to assess the best candidate. Within in the project GlycoWorkbench is used for the annotation of MS data. Subsequently GlycoWorkbench data files are used to import this annotation into the database.  EUROCarbDB can be synchronized with GlycomeDB  Synchronization allows updating EUROCarbDB with structure references to external databases  External databases are GlycomeDB, GLYCOSCIENCES.de, CarbBank, CFG, BCSDB, KEGG, GlycoBase, PDB [3]  These references are used to create Hyperlinks to these databases Figure 4: Workflow for the mzXML file upload (left) and the GlycoWorkbench data file upload (right) Figure 6:Select a created acquisition Figure 7:Upload GWB file for that acquisition Figrue 8: View or download the annotations Figure 5: Creating an acquisition based on mzXML files The workflow of this uploading system started with uploading a mzXML file to create an acquisition. Then any user can upload his annotation to this acquisition by uploading an appropriate GlycoWorkbench data file through our uploading system. Furthermore users can show any annotation and export it again into a GlycoWorkbench data file. Mass Spectrometry upload workflow Live connection to other databases Figure2 : Annotation comparison Figure 3: Importing database references via GlycomeDB and linking back to the databases We thank the original EUROCarbDB developers for their work and for sharing their source code with the community (http://code.google.com/p/eurocarb/). We especially thank Kai Maass (University Giessen) for his support and advice in the development of the mass spectrometry upload workflow. We also would like to thank the Consortium for Functional Glycomics for their support of this Bridging Grant.