1 Faculty of Science, SDU2 Department of Biochemistry and Molecular Biology, Faculty of Science, SDU3 Department of Biochemistry and Molecular Biology, Faculty of Science, SDU
We have developed "GLYCANthrope " - CROSSWORKS for glycans: a bioinformatics tool, which assists in identifying N-linked glycosylated peptides as well as their glycan moieties from MS2 data of enzymatically digested glycoproteins. The program runs either as a stand-alone application or as a plug-in for CROSSWORKS: our tool for investigating protein interaction and structure from MS data of chemically cross-linked proteins. The program can utilise mass spectrometric data fragmented by CID, ETD and HCD in the standard .mgf format - alone or in combination. We have investigated the efficiency of GLYCANthrope by searching CID and ETD MS2 data from a mixture of six known glycoprotins: Fetuin, RNAse1, Transferrin, a1-acid-glycoprotein, Ovalbumin and Ovomucoid. The glycopeptides and N-linked glycans reported by the program were then compared to the previously reported observations. The algorithm correctly identified all glycopeptides and suggested glycan structures for 10 out of 11 glycans, which were in agreement with earlier observations. We further observed previously undrescribed glycan structures for Ribonuclease, Asn60.
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2009Comparison of methods for selecting the midventilation bin in 4dct, 2009