Design Study 3  (MS- and HPLC: Standards and Tools for Spectrum Interpretation)

Objectives

• Creation of common standards for MS- and HPLC data (
• Creation of procedures and algorithms for the automatic inclusion of MS spectra and
  
• HPLC profiles into the prototype database
  
• Feasibility study how reliably calculated fragmentation patterns derived online from glycan sequences enable a safe automatic assignment of mass spectra
  
• Feasibility study how reliably HPLC profiles can be used enable a safe automatic annotation of glycans
  
• Preparation of manuals, tutorials and guideline for user input and retrieval options

Current status

Being highly sensitive methods, Mass Spectrometry (MS) and High Pressure Liquid Chromatography (HPLC) approaches are increasingly applied to provide information on the glycan repertoire of cells, tissues and organs. MS-spectra and HPLC coupled with appropriate databases of glycan structures will enable the automated assignment of the carbohydrate moieties of glycoproteins. However, no larger, publicly available depository of experimentally determined MS spectra of glycans is currently available. Moreover, no standardized procedures and agreements on quality measures exists, which have to be fulfilled before experimental data can enter the database. It is the aim of DS3-T1 and DS3-T2 to summarise the current status of definitions and guidelines used in glycobiology. DS3-T3 and DS3-T6 are oriented to demonstrate how the data flow of experimental data from the spectrometer to the database can be done using automatic procedures. Currently, the lack of fully automatic procedures, which reliably detect the glycan repertoire contained in MS spectra and HPLC profiles, is the largest obstacle for the upcoming glycomics projects to speed up the assignment procedures for glycan structures. It is the aim of DS3-T3, DS3-T4 and DS3-T5 to improve this unfavourable situation.
The HUPO Proteomics Standards Initiative (PSI) defines community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The PSI Mass Spectrometry work group develops a standard representation of experimental spectra in the context of the experimental setup and the analysed system. Such a format will allow supporting publications with detailed experimental results, and will allow data exchange and the comparison of related proteomics experiments beyond the local research team.
Several algorithms for semi-automatic interpretation of MS spectra have recently been reported aiming to aid the so far manually done assignment of MS and MSn spectra. The published solutions use either databases of known glycan structures or are purely theoretical de novo approaches, seeking to determine oligosaccharide structures incrementally, monosaccharide by monosaccharide, from the fragments observed. DS3-T3 will - based on the survey compiled in DS3-T2 – develop approaches for the rapid and reliable assignment of MS-spectra and HPLC profiles based on known glycan structures. DS3-T5 will implement the agreed procedures and algorithms. DS3-T7 will analyse the reliability, stability and reproducibility of procedures implemented during this design study.

EuroCarbDB is a Research Infrastructure Design Study Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)