PXD072999 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | DDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics |
| Description | This project provides a large-scale training dataset for DDA-BERT, an end-to-end transformer-based deep learning model developed for PSM rescoring in data-dependent acquisition (DDA) proteomics. The dataset comprises curated PSMs generated using established database search engines, including FragPipe, Sage, and AlphaPept, and is intended to support the training of the DDA-BERT model. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-08-24 |
| AnnouncementXML | Submission_2026-08-23_19:09:25.208.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Jun A |
| SpeciesList | scientific name: Bacillus subtilis; NCBI TaxID: NEWT:1423; scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Chlamydomonas reinhardtii; NCBI TaxID: NEWT:3055; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090; scientific name: Rattus norvegicus (Rat); NCBI TaxID: NEWT:10116; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932; scientific name: Escherichia coli; NCBI TaxID: NEWT:562; scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: NEWT:3702; scientific name: Caenorhabditis elegans; NCBI TaxID: NEWT:6239; scientific name: Bacillus cereus; NCBI TaxID: NEWT:1396; scientific name: Glycine max; NCBI TaxID: NEWT:3847; |
| ModificationList | S-carboxamidoethyl-L-cysteine; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
| Instrument | Orbitrap Eclipse; Q Exactive HF; Orbitrap Fusion Lumos; Orbitrap Exploris 480; Orbitrap Fusion ETD; PinPoint; Q Exactive HF-X; Q Exactive; Orbitrap Fusion; LTQ Orbitrap |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2026-01-13 01:38:07 | ID requested | |
| ⏵ 1 | 2026-08-23 19:09:26 | announced | |
Publication List
| A J, Liu P, Sun Y, Lin J, Zhang X, Nie Z, Liu J, Yu Z, Zhang Y, Xing Z, Chen Y, Guo T, DDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics. Nat Commun, 17(1):(2026) [pubmed] |
| 10.1038/s41467-026-72246-6; |
Keyword List
| submitter keyword: Deep learning, DDA proteomics, Peptide-spectrum matches (PSMs) rescoring, DDA-BERT, peptide identification |
Contact List
| Tiannan Guo |
|---|
| contact affiliation | Westlake University |
| contact email | guotiannan@westlake.edu.cn |
| lab head | |
| Jun A |
|---|
| contact affiliation | Westlake University |
| contact email | ajun@westlake.edu.cn |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD072999 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD072999
- Label: PRIDE project
- Name: DDA-BERT: end-to-end training for data-dependent acquisition mass spectrometry-based proteomics
