DecoyDeveloper: An On-Demand, De Novo Decoy Glycopeptide Generator

Glycopeptide analysis
is a growing field that is struggling to
adopt effective, automated tools. Many creative workflows and software
apps have emerged recently that offer promising capabilities for assigning
glycopeptides to MS data in an automated fashion. The effectiveness
of these tools is best measured and improved by determining how often
they would select a glycopeptide decoy as a spectral match, instead
of its correct assignment; yet generating the appropriate number and
type of glycopeptide decoys can be challenging. To address this need,
we have designed DecoyDeveloper, an on-demand decoy glycopeptide generator
that can produce a high volume of decoys with low mass differences.
DecoyDeveloper has a simple user interface and is capable of producing
large sets of decoys containing complete, biologically relevant glycan
and peptide sequences. We demonstrate the tool’s efficiency
by applying it to a set of 80 glycopeptide targets. This tool is freely
available and can be found at http://glycopro.chem.ku.edu/J1.php.