PXD071819 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | SoftHybrid: A Hybrid Imputation Algorithm Optimised for Single-Cell Proteomics Data |
| Description | Missing values (MVs) remain a significant barrier to reliable proteomics analysis, particularly in single-cell proteomics, where small amounts of starting material and limits in detection drive Missing-Not-At-Random (MNAR) sparsity. Commonly used bulk proteomic imputation approaches typically address Missing-At-Random (MAR) MVs and improve replicate consistency at the expense of sensitivity for biological variation, whereas MNAR-specific strategies preserve group differences but compromise cross-replicate reproducibility. Existing imputation methods are commonly applied to bulk data and do not offer a generalised ‘off-the-shelf’ implementation that robustly addresses the significant sparsity observed in single-cell studies. Here, we introduce SoftHybrid, a continuous weighting framework that automatically balances MAR- and MNAR-oriented imputation across a dataset-derived model between missing rate and protein abundance model. Benchmarking across known ground truth samples (three-species mix) and real single-cell proteomics data showed that SoftHybrid outperforms existing methods at low inputs while meeting or exceeding previous state-of-the-art performance at the mini-bulk level. Preservation of proteomic patterns and enhanced replicate consistency improve testing significance and boost recovery of biological signals. SoftHybrid is implemented as an R package and freely available on GitHub. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-07-24 |
| AnnouncementXML | Submission_2026-07-23_19:11:36.607.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Yixin Shi |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF Ultra 2 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-12-10 09:46:50 | ID requested | |
| ⏵ 1 | 2026-07-23 19:11:37 | announced | |
Publication List
Keyword List
Contact List
| Roman Fischer |
|---|
| contact affiliation | Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford |
| contact email | roman.fischer@ndm.ox.ac.uk |
| lab head | |
| Yixin Shi |
|---|
| contact affiliation | University of Oxford |
| contact email | yixin.shi@wolfson.ox.ac.uk |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD071819
- Label: PRIDE project
- Name: SoftHybrid: A Hybrid Imputation Algorithm Optimised for Single-Cell Proteomics Data
