Enhanced Sensitivity

Integrated glycan de novo sequencing and glycopeptide database search provides an increased sensitivity of glycopeptide identifications while allowing for the discovery of hidden glycopeptides. Evaluating each MS2 spectrum using two independent approaching results in superior confidence and increased glycoproteome depth.

Enhanced Structure Confidence

GlycanFinder performs structure-based glycopeptide identification. The S-Score (%) indicates how strongly the selected glycopeptide structure is supported compared with other isomeric glycan candidates—those sharing the same composition but differing in structure.

Glycan de novo

Glycan de novo sequencing enables the discovery of glycopeptides containing rare or unexpected glycans. The example below from an insect dataset highlights this capability.

InChorus

PEAKS GlycanFinder addresses the challenge of varying glycopeptide identifications between different search engines with its powerful new InChorus feature. InChorus integrates results from multiple glycan search engines to highlight consensus and unique hits, visualise overlaps, and provides a Consensus score, a metric which indicates glycopeptide spectral match consistency.

Multi-O Glycan Search

GlycanFinder supports searching up to five O-linked glycans on a single peptide, enabling identification of highly decorated O-glycopeptides. Despite the expanded combinatorial search space, GlycanFinder applies efficient filtering, site-specific localisation scoring, and structure-aware matching to maintain fast performance and deliver confident assignments.

Paired Spectra Support

The new HCD-pd-EThcD acquisition method delivers high-confidence glycan structure and site assignment. A new paired spectra display provides intuitive, side-by-side interpretation.

Glycan Modification

Glycan modifications such as phosphorylation broaden glycan diversity and may signal disease. PEAKS GlycanFinder provides comprehensive analysis of glycopeptides and released glycans with diverse glycan modifications.

Superior Reproducibility by Charge Lookup

Charge lookup increases reproducibility by incorporating all precursor features, including those lacking MS2 identification. Peptides frequently generate multiple charge states, and relying solely on identified precursors can bias glycan profiling. Charge lookup detects additional related precursors and uses the combined feature area for profiling.

Customisable Glycan Database

The glycan database editor enables users to build their own glycan databases through an intuitive user interface. Users can add, edit, and modify glycan structures through a drawing board and easily import them into the software.

Glycan Network

Glycan network provides an intuitive illustration of biosynthetic network relationships among various glycan compositions, where each edge connects two glycans that differ by only one monosaccharide. This makes it easy to visualise the different sugars extending from a common core structure.

Glycosylated Peptidome

Our Glycosylated Peptidome workflow is capable of the discovery and characterisation of completely novel glycans for immunopeptidomics, without the need for a glycan database. A recent study demonstrated that GlycanFinder was able to discovery an N-glycosylated peptide as a putative biomarker of drug resistance in doxorubicin resistance breast cancer cell line.

Vendor Neutral Software

For the best glycopeptide identification performance, GlycanFinder supports diverse instruments by integrating optimised algorithms trained on different fragmentation methods.