PXD069898 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Spectral Cruncher: A Visualization Tool Integrating Manual Curation, Ion-Intensity Prediction, and De Novo Tag Generation |
| Description | Here's a suggested Project Description for your PRIDE submission: Project Description This dataset contains mass spectrometry raw files used as training data for SpecFormer, a transformer-based ion intensity prediction model integrated within PatternLab for Proteomics (Spectral Cruncher module). The dataset includes bulk proteomics data from HeLa cells and Mus musculus (C57BL/6) kidney tissue, as well as single-cell proteomics data from WT83 human brain organoids acquired using the cellenOne platform. All samples were analyzed on an Orbitrap Astral mass spectrometer using data-dependent acquisition (DDA). These raw files were used to train instrument-specific models for accurate fragment ion intensity prediction in both bulk and single-cell proteomics workflows. The SpecFormer model and analysis tools described in this dataset are freely available within PatternLab 5.1 at http://patternlabforproteomics.org/51. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-02-16 |
| AnnouncementXML | Submission_2026-02-15_17:59:18.355.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Paulo Carvalho |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Orbitrap Astral |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-10-25 00:13:30 | ID requested | |
| ⏵ 1 | 2026-02-15 17:59:19 | announced | |
Publication List
| Martins AAM, Tsu BL, Brum H, Sales L, Mariano Dos Santos MD, Fischer JSDG, Almeida S, Vieira Coelho LB, Moreira N, Muotri AR, Carvalho PC, Spectral Cruncher: A Visualization Tool Integrating Manual Curation, Ion-Intensity Prediction, and De Novo Tag Generation. J Am Soc Mass Spectrom, 37(2):387-395(2026) [pubmed] |
| 10.1021/jasms.5c00301; |
Keyword List
| submitter keyword: ion intensity prediction, multi-species omics,single-cell proteomics |
Contact List
| Paulo Costa Carvalho |
|---|
| contact affiliation | Laboratory for Structural and Computational Proteomics; Fiocruz - Paraná |
| contact email | paulo@pcarvalho.com |
| lab head | |
| Paulo Carvalho |
|---|
| contact affiliation | Fiocruz |
| contact email | paulo@pcarvalho.com |
| 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/2026/02/PXD069898 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD069898
- Label: PRIDE project
- Name: Spectral Cruncher: A Visualization Tool Integrating Manual Curation, Ion-Intensity Prediction, and De Novo Tag Generation
