Introduction

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.

Publications

  1. GlycoMiner: a new software tool to elucidate glycopeptide composition.
    Cite this
    Ozohanics O, Krenyacz J, Ludányi K, Pollreisz F, Vékey K, Drahos L, 2008-10-01 - Rapid communications in mass spectrometry : RCM

Credits

  1. Oliver Ozohanics
    Developer

  2. Judit Krenyacz
    Developer

  3. Krisztina Ludányi
    Developer

  4. Ferenc Pollreisz
    Developer

  5. Károly Vékey
    Developer

  6. László Drahos
    Investigator

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Summary
AccessionBT002544
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByLászló Drahos