PXD065896
PXD065896 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | AlphaDIA enables DIA Transfer Learning for Feature-Free Proteomics |
| Description | The scale of data generated for mass spectrometry-based proteomics as well as modern acquisition strategies pose a challenge to bioinformatic analysis. Search engines need to make optimal use of the data for biological discoveries while remaining statistically rigorous, transparent and performant. Here we present alphaDIA, a modular open-source search framework for data independent acquisition (DIA) proteomics. We developed a feature-free identification algorithm that performs machine learning directly on the raw signal and is particularly suited for detecting patterns in data produced by time-of-flight instruments. Benchmarking demonstrates competitive identification and quantification performance. While the method supports empirical spectral libraries, we propose a search strategy named DIA transfer learning that uses fully predicted libraries. This entails continuously optimizing a deep neural network for predicting machine- and experiment-specific properties, enabling the generic DIA analysis of any post-translational modification. AlphaDIA provides a high performance and accessible framework running locally or in the cloud, opening DIA analysis to the community. |
| HostingRepository | MassIVE |
| AnnounceDate | 2025-07-08 |
| AnnouncementXML | Submission_2025-07-08_05:19:01.391.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Georg Wallmann |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | Carbamidomethyl |
| Instrument | Orbitrap Astral |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2025-07-08 05:07:33 | ID requested | |
| ⏵ 1 | 2025-07-08 05:19:01 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: search engine, DatasetType:Proteomics |
Contact List
| Matthias Mann | |
|---|---|
| contact affiliation | Proteomics and Signal Transduction Max Planck Institute of Biochemistry Am Klopferspitz 18 D-82152 Martinsried |
| contact email | mmann@biochem.mpg.de |
| lab head | |
| Georg Wallmann | |
| contact email | wallmann@biochem.mpg.de |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| 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://massive-ftp.ucsd.edu/v10/MSV000098448/ |
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