title: GlycoPep Detector: a tool for assigning mass spectrometry data of N-linked glycopeptides on the basis of their electron transfer dissociation spectra.
abstract: Electron transfer dissociation (ETD) is commonly used in fragmenting N-linked glycopeptides in their mass spectral analyses to complement collision-induced dissociation (CID) experiments. The glycan remains intact through ETD, while the peptide backbone is cleaved, providing the sequence of amino acids for a glycopeptide. Nonetheless, data analysis is a major bottleneck to high-throughput glycopeptide identification based on ETD data, due to the complexity and diversity of ETD mass spectra compared to CID counterparts. GlycoPep Detector (GPD) is a web-based tool to address this challenge. It filters out noise peaks that interfere with glycopeptide sequencing, correlates input glycopeptide compositions with the ETD spectra, and assigns a score for each candidate. By considering multiple ion series (c-, z-, and y-ions) and scoring them separately, the software gives more weighting to the ion series that matches peaks of high intensity in the spectra. This feature enables the correct glycopeptide to receive a high score while keeping scores of incorrect compositions low. GPD has been utilized to interpret data collected on six model glycoproteins (RNase B, avidin, fetuin, asialofetuin, transferrin, and AGP) as well as a clade C HIV envelope glycoprotein, C.97ZA012 gp140ΔCFI. In every assignment made by GPD, the correct glycopeptide composition earns a score that is about 2-fold higher than other incorrect glycopeptide candidates (decoys). The software can be accessed at http://glycopro.chem.ku.edu/ZZKHome.php .
authors.affiliation: Department of Chemistry, University of Kansas, Lawrence, Kansas 66047, United States.
authors.forename: Zhikai
authors.initials: Z
authors.lastname: Zhu
authors.forename: David
authors.initials: D
authors.lastname: Hua
authors.forename: Daniel F
authors.initials: DF
authors.lastname: Clark
authors.forename: Eden P
authors.initials: EP
authors.lastname: Go
authors.forename: Heather
authors.initials: H
authors.lastname: Desaire
mesh_terms: D000595:Amino Acid Sequence; D004579:Electron Transport; D005189:False Positive Reactions; D006020:Glycopeptides / Q000032:analysis / Q000737:chemistry*; D006023:Glycoproteins / Q000737:chemistry; D020407:Internet; D013058:Mass Spectrometry / Q000379:methods*; D008969:Molecular Sequence Data; D009584:Nitrogen / Q000737:chemistry*; D010446:Peptide Fragments / Q000737:chemistry; D015203:Reproducibility of Results; D012984:Software; D013223:Statistics as Topic / Q000379:methods*
chemical_list: C033904:GP 140; D006020:Glycopeptides; D006023:Glycoproteins; D010446:Peptide Fragments; D009584:Nitrogen