PXD055981 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | High-throughput mixed-species quantitative benchmark with varying sample amounts |
| Description | Samples were generated by mixing commercially available tryptic digests (human: K562, HeLa; yeast (S.cerevisiae); E.coli) in defined proportions, to create a dataset with known ground truth, for benchmarking of the quantitative performance and scalability of DIA raw data processing software. Acquisition was performed in high throughput using the Evosep One system operated in microflow mode coupled to Bruker timsTOF Ultra in dia-PASEF mode. The experiment design is specified in the “Experiment_design.xlsx” file attached and achieves the following: - The human background is perturbed in a controlled manner, by mixing K562 and HeLa digests in defined proportions, to model the biological variation observed in applications. The E.coli digest within the samples serves for normalisation, whereas the yeast digest is added in different proportions relative to E.coli in different samples and therefore allows the evaluate the quantitative accuracy of the method. - The scale of the experiment allows to evaluate the effect of the number of samples on the quantitative performance of the software. - The experiment involves acquisitions with medium-high to very low load, modelling the rapidly emerging applications of high-sensitivity DIA proteomics. |
| HostingRepository | PRIDE |
| AnnounceDate | 2025-12-09 |
| AnnouncementXML | Submission_2025-12-09_09:33:14.408.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Vadim Demichev |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932; scientific name: Escherichia coli; NCBI TaxID: NEWT:562; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF Ultra |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2024-09-18 07:47:07 | ID requested | |
| ⏵ 1 | 2025-12-09 09:33:14 | announced | |
Publication List
Keyword List
Contact List
| Vadim Demichev |
|---|
| contact affiliation | Charité – Universitätsmedizin Berlin |
| contact email | vadim.demichev@gmail.com |
| lab head | |
| Vadim Demichev |
|---|
| contact affiliation | Charité – Universitätsmedizin Berlin |
| contact email | vadim.demichev@gmail.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/2025/12/PXD055981 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD055981
- Label: PRIDE project
- Name: High-throughput mixed-species quantitative benchmark with varying sample amounts
