Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics
peer-reviewed · Nature Communications · 2023
| Date | 2023-07-08 |
| Type | peer-reviewed |
| Venue | Nature Communications |
| Publisher | Nature Communications |
| Contribution | adjacent |
| DOI | 10.1038/s41467-023-39699-5 |
| Citations (OpenAlex) | 60 |
| Venue 2-year citedness | 15.88 |
Abstract
Here we present GlycanFinder, a database search and de novo sequencing tool for the analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates peptide-based and glycan-based search strategies to address the challenge of complex fragmentation of glycopeptides. A deep learning model is designed to capture glycan tree structures and their fragment ions for de novo sequencing of glycans that do not exist in the database. We performed extensive analyses to validate the false discovery rates (FDRs) at both peptide and glycan levels and to evaluate GlycanFinder based on comprehensive benchmarks from previous community-based studies. Our results show that GlycanFinder achieved comparable performance to other leading glycoproteomics softwares in terms of both FDR control and the number of identifications. Moreover, GlycanFinder was also able to identify glycopeptides not found in existing databases. Finally, we conducted a mass spectrometry experiment for antibody N-linked glycosylation profiling that could distinguish isomeric peptides and glycans in four immunoglobulin G subclasses, which had been a challenging problem to previous studies.
Methods and tools
- GlycanFinder: Glycopeptide sequencing
Cites (4)
- Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices (2021) both
- Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry (2018) both
- De novo peptide sequencing by deep learning (2017) both
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2012) crossref
Cited by (3)
- Modanovo: A Unified Model for Post-translational Modification-Aware De Novo Sequencing Using Experimental Spectra From In Vivo and Synthetic Peptides (2025) both
- Modanovo: A Unified Model for Post-Translational Modification-Aware de Novo Sequencing Using Experimental Spectra from In Vivo and Synthetic Peptides (2025) both
- An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra (2025) crossref