GlycoWorkbench? GlycanBuilder ExampleDataSets VersionChanges ShortManual AuthorsContact


ExampleDataSets

The installation file contains a folder named examples where you find some sample files to test the annotation features of the tool. In each sub-folder you will find sample structures together with their fragment peak lists. To test the annotation process just open the structure file inside GlycoWorkbench? and load its corresponding peak list.

Set 1

The structures and peak lists contained in this set have been retrieved from:

Y. Mechref and M.V. Novotny,Structural Characterization of Oligosaccharides Using Maldi-TOF/TOF Tandem Mass Spectrometry, Analytical Chemistry, Volume 75, Issue 18, 4895 - 4903, 2003.

The peak lists have been obtained by running the underivatized structures trough a MALDI-TOF/TOF equipment. To obtain the same mass values the options "underivatized" and "Na+" ion must be selected in the Mass options dialog.

Set 2

The structures and peak lists contained in this set have been retrieved from:

E. Spina, L. Sturiale, D. Romeo, et al, New fragmentation mechanisms in matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry of carbohydrates, Rapid Communications in Mass Spectrometry, Volume 18, Issue 4, Pages 392-398, 2004.

Set 3

This set contains various structure files that show the display of different types of structures.

GAGs

This folder contains a workspace file showing a complete assignment of mass spectrometry data for a heparin oligosaccharide. A sample containing a mixture of dp10 oligosaccharide has been analysed by MS and MS/MS both in norharmane and ionic liquid. More details of the experimental setup can be found in.

B. Tissot, N. Gasiunas, A.K. Powell, et al, Towards GAG glycomics: Analysis of highly sulfated heparins by MALDI-TOF mass spectrometry, Glycobiology Volume 17, Pages 972-982, 2007.