Journal
PROTEOMICS
Volume 7, Issue 24, Pages 4435-4444Publisher
WILEY
DOI: 10.1002/pmic.200700253
Keywords
backtracking algorithm; freely available software; glycan composition analysis; mass spectrometry; (semi-)automated annotation
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Mass spectrometric techniques are the key technology for rapid and reliable glycan analysis. However, the lack of robust, dependable, and freely available software for the (semi-) automatic annotation of mass spectra is still a severe bottleneck that hampers their rapid interpretation. In this article the Glyco-Peakfinder web-service is described allowing de novo determination of glycan compositions from their mass signals. Starting from a basic set of mandatory masses of glycan components, the calculation can be performed without any knowledge concerning the biological background of the sample or the fragmentation technique used. Glyco-Peakfinder assigns all types of fragment ions including monosaccharide cross-ring cleavage products and multiply charged ions. It provides full user control to handle modified glycans (persubstituted molecules, reducing-end modifications, glycoconjugates) and ion types. The formula applied to calculate the fragment masses and an outline of the implemented algorithm are discussed. A systematic evaluation of the dependence of all factors influencing the computation time revealed strikingly different impact of the individual calculation steps. To provide access to known carbohydrate structures a composition search in the open access database GLYCOSCIENCES.de can be performed. The service is available at the URL: www.eurocarbdb.org/applications/ms-tools.
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