Combinatorics

Graph

Glycan

Mathematics

Antibiotics

Biology

Glycoprotein

Algorithm

Search algorithm

Glycoproteomics

Glycopeptide

Chemistry

Information retrieval

Computer science

Computational biology

Theoretical computer science

Database search engine

Biochemistry

Search engine

Nature Methods

We report O-Pair Search, an approach to identify O-glycopeptides and localize O-glycosites. Using paired collision- and electron-based dissociation spectra, O-Pair Search identifies O-glycopeptides via an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization. O-Pair Search reduces search times more than 2,000-fold compared to current O-glycopeptide processing software, while defining O-glycosite localization confidence levels and generating more O-glycopeptide identifications. Beyond the mucin-type O-glycopeptides discussed here, O-Pair Search also accepts user-defined glycan databases, making it compatible with many types of O-glycosylation. O-Pair Search is freely available within the open-source MetaMorpheus platform at                 https://github.com/smith-chem-wisc/MetaMorpheus                              . O-Pair search identifies O-glycopeptides and localizes O-glycosites using a fragment-ion-indexed open modification search combined with a graph-based approach. It also introduces a classification scheme to unify data reporting for glycoproteomics.

O-Pair Search with MetaMorpheus for O-glycopeptide characterization