⮝ Full datasets listing
PXD080865
PXD080865 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Recovering biological structure in sparse single-cell proteomics with GIRAFI |
| Description | Single-cell proteomics (SCP) based on liquid-chromatography mass-spectrometry resolves protein-level cellular heterogeneity, but interpretation remains limited by detection-linked sparsity. SCP profiles continuous, peptide-derived intensities and has lower throughput than single-cell RNA sequencing, making denoising methods for large-scale, count-based transcriptomics difficult to apply. Here we present GIRAFI, a graph-informed statistical learning framework that imputes missing values and reveals reproducible cell states by constraining inference to dataset-aware, prior-knowledge-informed protein neighborhoods. We evaluated GIRAFI across SCP datasets spanning diverse biological/technical contexts. In masking-based recovery experiments and cell-type-specific protein-protein interaction inference, GIRAFI outperformed existing methods, and matched bulk proteomics comparisons corroborated recovery accuracy and ablations supported the graph-informed design. Beyond reduced replicate- and source-associated technical structure, GIRAFI recovered ground-truth cell-type annotations, improved cell state-resolved pathway analysis, and enabled trajectory inference consistent with known time courses. These results establish graph-constrained imputation as an effective strategy for improving SCP robustness, biological structure, interpretation, and cross-dataset comparability. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-08-10 |
| AnnouncementXML | Submission_2026-08-10_17:11:50.448.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Shuxin Chi |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; scientific name: Apis mellifera; common name: honey bee; NCBI TaxID: 7460; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF SCP; timsTOF Ultra 2 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-07-10 12:50:33 | ID requested | |
| ⏵ 1 | 2026-08-10 17:11:50 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Single-cell Proteomics, Data imputation, Data analysis, DatasetType:Proteomics |
Contact List
| Leonard J. Foster | |
|---|---|
| contact affiliation | Michael Smith Laboratories, Biochemistry and Molecular Biology, University of British Columbia, Canada |
| contact email | foster@msl.ubc.ca |
| lab head | |
| Shuxin Chi | |
| contact affiliation | University of British Columbia |
| contact email | lucyc910@student.ubc.ca |
| 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/v13/MSV000102427/ |
