New computer software, GlycoMiner, has been developed to automatically identify tandem (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 under Windows, 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.

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Post-translational modifications controlling a large number of biological functions are key aspects of protein diversity. They have an important role controlling cellular processes and may be advantageously utilized. Qualitative and quantitative analyses of post-translational modifications are useful for biomarker research and an integral part of the characterization of protein biopharmaceuticals. Due to its sensitivity and widespread applicability, mass spectrometry has become the core technology of the analysis especially when combined with chromatographic and other separation techniques. The aim of this article is to present a general overview of mass spectrometry applications in the field of PTM mapping. We also present the analytical challenges of particular PTMs, primarily focusing on the most frequent modifications.

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