⮝ Full datasets listing
PXD073851-1
PXD073851 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Bridging Simplicity and Depth in Single-Cell Proteomics: A Cost-Effective Workflow and Expanded Framework for Data Evaluation |
| Description | Single-cell proteomics (SCP) offers direct insight into functional protein states that drive cellular heterogeneity, complementing genomic and transcriptomic analyses. Although recent reports have demonstrated improved proteome coverage, their reliance on specialized instrumentation limits broader adoption. Additionally, current evaluation practices remain largely centered on protein and peptide identification counts, which alone do not fully reflect data quality or biological interpretability. Here, we describe an accessible, label-free SCP workflow which implements easily accessible laboratory equipment: a single-cell dispenser, conventional multiwell plates, and an incubator with water-bath-based humidity control. Using trapped ion mobility spectrometry-time-of-flight mass spectrometry (timsTOF), we systematically optimize key sample preparation variables, including trypsin concentration, incubation time, reduction/alkylation, digestion conditions, and plate types, which together maximize data quality and reproducibility. We further introduce a data-quality framework that moves beyond identification counts, emphasizing quantitative consistency and biological interpretability via individual protein coverage completeness across cells, coefficients of variation across technical replicates, peptide-to-protein ratios, and single-cell-to-bulk correlations. Collectively, our approach lowers technical barriers to accessing SCP while enabling more rigorous, interpretable, and scalable SCP analysis across diverse research contexts. |
| HostingRepository | MassIVE |
| AnnounceDate | 2026-07-07 |
| AnnouncementXML | Submission_2026-07-07_16:39:18.224.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: Rattus norvegicus; common name: Norway rat; NCBI TaxID: 10116; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF SCP |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2026-01-30 10:11:07 | ID requested | |
| ⏵ 1 | 2026-07-07 16:39:18 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: Single-cell Proteomics, mass spectrometry, timsTOF, 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/v12/MSV000100666/ |
