NIH Proteomics Interest Group

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ProtIG is an NIH Special Interest Group (SIG) that organizes seminars and workshops in relevant areas of proteomics, including talks on separation and protein identification methods, determination of post-translational modifications, protein-protein interactions, and bioinformatics and data management. A monthly seminar series is usually held at 11am on the first Wednesday of each month (always check the Mtgs/Seminars button on this page for these and other PROTIG announced meetings). To receive email announcements of ProtIG events, join the listserv (Join the SIG button on this page)

November ProtIG Seminar
Please note the time and location
November 2nd, 2017
9:30 am - 10:30am
Building 50, NIH Campus
Room 1328/1334 (Rear Conference Room)
Nathan Edwards, Ph.D
Associate Professor
Department of Biochemistry and Molecular and Cellular Biology
Georgetown University, Washington, DC

"Site-specific Glycopeptide Identification by Tandem Mass Spectrometry"

The characterization of intact glycopeptides by tandem mass spectrometry has significant potential for elucidating site-specific glycosylation of proteins, providing insight into perturbed disease, tissue, subcellular location, and other context dependent glycosylation pathways. However, there are substantial informatics challenges that must be solved to meet this promise. The GlycoPeptideSearch (GPS) tool, developed for CID tandem mass spectra of intact glycopeptides, uses a novel decoy strategy to estimate glycopeptide false discovery rates, and seeks to characterize distinct glycan structures on peptide substrates, not just monosaccharide composition. Importantly, the focus on glycan structures requires careful handling of glycopeptides that may or may not be readily distinguishable by tandem mass spectrometry, and has led to work on describing the relationships between partially described or characterized glycan structures. We are currently extending GPS to take advantage of advanced mass-spectrometry fragmentation techniques, such as HCD triggered ETD (HCDpdETD), combined ETD/HCD fragmentation (EThcD), and multi-collision energy spectra. In each case, these multi-spectra observations from the same precursor ion require new informatics strategies, and, in particular, new FDR estimation techniques. We have implemented a lattice-based multi-metric FDR estimation technique suitable for multi-spectra, multi-fragmentation mode workflows that demonstrates significant improvement over fixed filtering approaches. Lastly, we apply precursor mass-delta tolerant spectral matching to build spectral networks of glycopeptide tandem mass-spectra so that high confidence glycopeptide identifications can be used to make glycopeptide assignments to related spectra. We hope that together, these strategies will soon make glycopeptide identification by tandem mass spectrometry as routine and informative as peptide identification from bottom-up proteomics workflows.

Seminars will be webcast online at and available on the
Proteomics Interest Group website as an archived presentation unless otherwise noted.

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This site was updated on November 1st, 2017. Please contact Renee Olano at olanol(at) with questions or suggestions.