⮝ Full datasets listing
PXD063217-1
PXD063217 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | XL-MSDigger: A Computational Pipeline for In-Depth Data Analysis and Mining of Cross-Linking Mass Spectrometry |
| Description | Cross-linked mass spectrometry (XL-MS) plays an increasing role in the study of protein structure and protein-protein interactions, but the development of its data analysis methods is currently lagging that of conventional proteomics, especially in terms of artificial intelligence-based analysis and data-independent acquisition (DIA) methods. Here, we constructed Deep4D-XL, a deep learning tool capable of accurately predicting crosslinked peptide 4D information. Using Deep4D-XL as the core, we developed XL-MSDigger, a deep-learning-based pipeline for comprehensive data analysis of crosslinked mass spectrometry, which can realize deep analysis of cross-linked mass spectrometry DDA and DIA data. In the DDA data analysis of Hela crosslinked samples, we improved the identification of inter-protein crosslinked peptides by 62% through the rescoring method of XL-MSDigger. In DIA analysis, we realized the first FDR evaluation of DIA XL-MS and DIA XL-MS analysis based on predicted spectral libraries. In the analysis of heat shock protein PPI networks, DIA XL-MS based on predicted spectral libraries exhibited higher identification coverage than the DDA method. We anticipate that XL-MSDigger will play a pivotal role in advancing future XL-MS research. |
| HostingRepository | iProX |
| AnnounceDate | 2025-04-23 |
| AnnouncementXML | Submission_2026-01-25_16:34:38.113.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Moran Chen |
| SpeciesList | scientific name: Homo sapiens; NCBI TaxID: 9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF Pro |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-04-22 21:51:28 | ID requested | |
| ⏵ 1 | 2026-01-25 16:34:38 | announced |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: XL-MS, Deep learning, DDA, DIA |
Contact List
| Suming Chen | |
|---|---|
| contact affiliation | The Institute for Advanced Studies, Wuhan University |
| contact email | chensm@iccas.ac.cn |
| lab head | |
| Moran Chen | |
| contact affiliation | The Institute for Advanced Studies, Wuhan University |
| contact email | 1019524103@qq.com |
| dataset submitter | |
Full Dataset Link List
| iProX dataset URI |
