Objectives
Description of DS3-T1
Based on the knowledge accumulated in the partners’ labs and an intensive survey of the literature a report on existing standards and formats for MS-spectra as well as associated separation procedures will be compiled. The survey will focus on the scientific importance of the experimental data with respect to ongoing glycomics projects, the technical requirements to enable an automatic inclusion of experimental data into a database and on identifying the already existing data collections and procedures in glycomics research. ICL and UGI will focus to summarise the definitions, conventions, standards for the representation of MS spectra and associated separation procedures.
Description of DS3-T2
A comprehensive survey of digital formats, the data flow of experimental data and algorithms for the automatic annotation and storage of MS spectra into databases will be assembled. This compilation will be based on the knowledge accumulated in the partners’ labs as well as on an intensive survey of the literature and the Internet. Eventually, some direct contacts to newly emerging databases and algorithms for the automatic interpretation of MS data may be necessary. DKFZ and ICL will focus to assemble and evaluate the content of available databases as well as the reliability and efficiency of algorithms in the realm of mass spectrometry.
Description of DS3-T3
Based on the survey compiled in DS3-T1 and DS3-T2, ICL, UGI and DKFZ will develop concepts and an implementation plan for the automatic flow of data from the recorded data on the spectrometer into the P2P network. ICL, UGI and DKFZ will work out the basic concepts and a detailed implementation plan for automatic MS-spectra interpretation.
Description of DS3-T4
Based on the knowledge accumulated in the partners’ labs and an intensive survey of the literature, guidelines for quality measures will be formulated, which have to be fulfilled before MS-spectra can enter the P2P network and subsequently the central database. To guarantee a broad acceptance of the approved quality agreements it will be considered to distribute a questionnaire to other well-known labs for glycan analysis using MS-techniques, to be sure that all aspects relevant for quality measure have been covered. ICL and UGI will draft quality measures for the inclusion of MS spectra. The implementation of the agreed quality measures into the P2P network and the central database will be accomplished by the respective partner and in close co-operation with DS2 partners.
Description of DS3-T5
Based on the survey compiled in DS3-T1 and DS3-T2 and the implementation plan drafted in DS3-T3 DKFZ will implement the algorithms and procedures, which will enable a reliable, automatic and rapid assignment of MS-spectra. ICL and UGI will provide appropriate, manually assigned MS spectra, which have been measured using various separation procedures and ionisation techniques. ICL and UGI will continuously evaluate the success of the automatic procedures, make suggestion how to improve the underlying algorithms, define experimental data which have to be added to make the procedures more general so that they can be applied to an increasing number of classes of glycans. Additionally, ICL and UGI will appoint the degree of fuzziness for experimental data which can be accepted to cope with varying separation and detection approaches.
Description of DS3-T6
Manuals and tutorials describing the data flow and retrieval options for MS spectra will be generated by ICL and UGI. . ICL and DKFZ will create manuals and tutorials, how to use the automatic assignment and interpretation procedures for MS spectra.
Description of DS3-T7
ICL and UGI will be performed an evaluation of the prototype of the P2P network for input, retrieval and interpretation of MS spectra. The analysis will be based on the experiences made by the partners in their own labs, a questionnaire which will be sent to selected labs outside the consortium and several internet forums, which will allow interested gylcoscientists to take part in the discussion, report their experiences made using the recommendations made by the consortium. Based on these experiences, recommendations will be formulated describing improvements and new features, which should be included into the fully functional version of the new infrastructure. ICL and UGI will evaluate the reliability of the automatic assignment routines for MS spectra and formulate recommendations for improvements, which should be included into a fully functional new infrastructure to optimise the data flow procedures as well as the reliability of the automatic assignment routines.
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
