What is this

GlycoMiner, has been developed to automatically identify MS/MS spectra obtained in LC-MS runs which correspond to N-glycopeptides. The program complements conventional proteomics analysis, and can be used in a high-throughput environment. It interprets the spectra and determines the structure of the corresponding glycopeptides. GlycoMiner
runs under Windows, can process spectra obtained on various instruments, if monoisotopic, singly charged spectra are supplied. The algorithm works similar to a human expert; evaluates the low mass oxonium ions; oligosaccharide losses from the molecular ion and identifies the mass of the peptide residue.

The program has been tested on tryptic digests of two glycopeptides; AGP (which has 5 different N-glycosylation sites) and transferrin (with 2 Nglycosylation 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. Out of these it was possible to identify the structure of 196 spectra manually; GlycoMiner correctly identified all of these, with no false positives.

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