Glycoproteomics

I Bagdonaite, SA Malaker, DA Polasky… - Nature Reviews …, 2022 - nature.com
Protein glycosylation involves the co-translational or post-translational addition of glycans to
proteins and is a crucial protein modification in health and disease. The aim of …

Recent advances in computational algorithms and software for large-scale glycoproteomics

DA Polasky, AI Nesvizhskii - Current Opinion in Chemical Biology, 2023 - Elsevier
Glycoproteomics, or characterizing glycosylation events at a proteome scale, has seen rapid
advances in methods for analyzing glycopeptides by tandem mass spectrometry in recent …

MSBooster: improving peptide identification rates using deep learning-based features

KL Yang, F Yu, GC Teo, K Li, V Demichev… - Nature …, 2023 - nature.com
Peptide identification in liquid chromatography-tandem mass spectrometry (LC-MS/MS)
experiments relies on computational algorithms for matching acquired MS/MS spectra …

Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides

DJ Geiszler, DA Polasky, F Yu, AI Nesvizhskii - Nature Communications, 2023 - nature.com
Post-translational modifications are an area of great interest in mass spectrometry-based
proteomics, with a surge in methods to detect them in recent years. However, post …

Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics

W Sun, Q Zhang, X Zhang, NH Tran… - Nature …, 2023 - nature.com
Here we present GlycanFinder, a database search and de novo sequencing tool for the
analysis of intact glycopeptides from mass spectrometry data. GlycanFinder integrates …

Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity

J Klein, L Carvalho, J Zaia - Nature Communications, 2024 - nature.com
Accurate glycopeptide identification in mass spectrometry-based glycoproteomics is a
challenging problem at scale. Recent innovation has been made in increasing the scope …

[HTML][HTML] N-glycoproteomics of brain synapses and synaptic vesicles

MM Bradberry, TM Peters-Clarke, E Shishkova… - Cell reports, 2023 - cell.com
At mammalian neuronal synapses, synaptic vesicle (SV) glycoproteins are essential for
robust neurotransmission. Asparagine (N)-linked glycosylation is required for delivery of the …

Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species

WF Zeng, G Yan, H Zhao, C Liu, W Cao - Nature Communications, 2024 - nature.com
Precision map** of site-specific glycans using mass spectrometry is vital in
glycoproteomics. However, the diversity of glycan compositions across species often …

Unraveling the glycosylated immunopeptidome with HLA-Glyco

G Bedran, DA Polasky, Y Hsiao, F Yu… - Nature …, 2023 - nature.com
Recent interest in targeted therapies has been sparked by the study of MHC-associated
peptides (MAPs) that undergo post-translational modifications (PTMs), particularly …

Deep learning prediction of glycopeptide tandem mass spectra powers glycoproteomics

Y Zong, Y Wang, X Qiu, X Huang, L Qiao - Nature Machine Intelligence, 2024 - nature.com
Protein glycosylation, a post-translational modification of proteins by glycans, plays an
important role in numerous physiological and pathological cellular functions …