GlycoMiner: a new software tool to elucidate glycopeptide composition

Ozohanovics, Olivér and Krenyácz, Judit and Ludányi, Krisztina and Pollreisz, Ferenc and Vékey, Károly and Drahos, László (2008) GlycoMiner: a new software tool to elucidate glycopeptide composition. RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 22 (20). pp. 3245-3254. ISSN 0951-4198

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Abstract

Newcomputersoftware,GlycoMiner, has been developed toautomatically identifytandem(MS/MS) spectra obtained in liquid chromatography/mass spectrometry (LC/MS) runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. The program interprets the spectra and determines the structure of the corresponding glycopeptides.GlycoMiner runs underWindows, can process spectra obtained on various instruments, and can be downloaded from our website (w3.chemres.hu/ms/glycominer). The algorithm works similarly to a human expert; evaluates the low mass oxonium ions; deduces oligosaccharide losses from the protonated molecule; and identifies the mass of the peptide residue. The program has been tested on tryptic digests of two glycopeptides: AGP (which has five different N-glycosylation sites) and transferrin (with two N-glycosylation sites). Results have been evaluated both manually and by GlycoMiner. Out of 3132 MS/MS spectra 338 were found to correspond to glycopeptides; identification by GlycoMiner showed a 0.1% false positive and 0.1% false negative rate. From these it was possible to identify 196 glycan structures manually; GlycoMiner correctly identified all of these, with no false positives. The rest were low quality spectra, not suitable for structure assignment. Copyright # 2008 John Wiley & Sons, Ltd.

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