PXD045248

PXD045248 is an original dataset announced via ProteomeXchange.

Title	Prediction of glycopeptide fragment mass spectra by deep learning
Description	Deep learning has achieved a notable success in mass spectrometry-based proteomics and is now emerging in glycoproteomics. While various deep learning models can predict fragment mass spectra of peptides with good accuracy, they cannot cope with the non-linear glycan structure in an intact glycopeptide. Herein, we propose a deep learning-based approach for the prediction of fragment spectra of intact glycopeptides. Our model adopts tree-structured long-short term memory networks to process the glycan moiety and a graph neural network architecture to incorporate potential fragmentation pathways of a specific glycan structure. This feature is beneficial to model explainability and differentiation ability of glycan structural isomers. We further demonstrated that predicted spectral libraries can be used for analyzing DIA data of glycopeptides as a supplement for library completeness. We expect that this work will provide a valuable deep learning resource for glycoproteomics.
HostingRepository	iProX
AnnounceDate	2023-12-17
AnnouncementXML	Submission_2024-02-20_00:43:51.973.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yi Yang
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606; scientific name: Mus musculus; NCBI TaxID: 10090; scientific name: Schizosaccharomyces pombe; NCBI TaxID: 4896; scientific name: Saccharomyces cerevisiae; NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue; oxidation; N-glycosylated residue
Instrument	Orbitrap Exploris 480; Orbitrap Fusion; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-11 00:05:53	ID requested
⏵ 1	2024-02-20 00:43:52	announced

Dataset with its publication pending

submitter keyword: glycopeptide, mass spectra prediction, deep learning

Yi Yang
contact affiliation	Zhejiang University
contact email	y_yi@zju.edu.cn
lab head
Yi Yang
contact affiliation	Zhejiang University
contact email	y_yi@zju.edu.cn
dataset submitter

iProX dataset URI