3 research outputs found
GlycoPep Grader: A Web-Based Utility for Assigning the Composition of <i>N</i>-Linked Glycopeptides
GlycoPep grader (GPG) is a freely available software
tool designed
to accelerate the process of accurately determining glycopeptide composition
from tandem mass spectrometric data. GPG relies on the identification
of unique dissociation patterns shown for high mannose, hybrid, and
complex <i>N</i>-linked glycoprotein types, including patterns
specific to those structures containing fucose or sialic acid residues.
The novel GPG scoring algorithm scores potential candidate compositions
of the same nominal mass against MS/MS data through evaluation of
the Y<sub>1</sub> ion and other peptide-containing product ions, across
multiple charge states, when applicable. In addition to evaluating
the peptide portion of a given glycopeptide, the GPG algorithm predicts
and scores product ions that result from unique neutral losses of
terminal glycans. GPG has been applied to a variety of glycoproteins,
including RNase B, asialofetuin, and transferrin, and the HIV envelope
glycoprotein, CON-S gp140ΔCFI. The GPG software is implemented
predominantly in PostgreSQL, with PHP as the presentation tier, and
is publicly accessible online. Thus far, the algorithm has identified
the correct compositional assignment from multiple candidate <i>N</i>-glycopeptides in all tests performed