Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides

The glycopeptide
analysis field is tightly constrained by a lack
of effective tools that translate mass spectrometry data into meaningful
chemical information, and perhaps the most challenging aspect of building
effective glycopeptide analysis software is designing an accurate
scoring algorithm for MS/MS data. We provide the glycoproteomics community
with two tools to address this challenge. The first tool, a curated
set of 100 expert-assigned CID spectra of glycopeptides, contains
a diverse set of spectra from a variety of glycan types; the second
tool, Glycopeptide Decoy Generator, is a new software application
that generates glycopeptide decoys de novo. We developed these tools
so that emerging methods of assigning glycopeptides’ CID spectra
could be rigorously tested. Software developers or those interested
in developing skills in expert (manual) analysis can use these tools
to facilitate their work. We demonstrate the tools’ utility
in assessing the quality of one particular glycopeptide software package,
GlycoPep Grader, which assigns glycopeptides to CID spectra. We first
acquired the set of 100 expert assigned CID spectra; then, we used
the Decoy Generator (described herein) to generate 20 decoys per target
glycopeptide. The assigned spectra and decoys were used to test the
accuracy of GlycoPep Grader’s scoring algorithm; new strengths
and weaknesses were identified in the algorithm using this approach.
Both newly developed tools are freely available. The software can
be downloaded at http://glycopro.chem.ku.edu/GPJ.jar