PXD048959
PXD048959 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Optimizing and integrating depletion and precipitation methods for plasma proteomics through data-independent acquisition-mass spectrometry |
| Description | The application of plasma proteomics is a reliable approach for the discovery of biomarkers. However, the utilization of mass spectrometry-based proteomics in plasma encounters limitations due to the presence of high-abundant proteins (HAPs) and the vast dynamic range. To address this issue, we conducted an optimization and integration of depletion and precipitation strategies eliminating interference from HAPs. The optimized procedure involved utilizing 40 µL of beads for the removal of 1 µL of plasma, and maintaining a ratio of 1:1:1 between plasma, urea, and trichloroacetic acid for the precipitation of 50 µL of plasma. To facilitate high-throughput processing, experimental procedures were carried out utilizing 96-well plates. The depletion method identified a total of 1510 proteins, whereas the precipitated method yielded a total of 802 proteins. The integration of these methods yielded a total of 1794 proteins, including a wide concentration range spanning over 8 orders of magnitude. Furthermore, these approaches exhibited a commendable level of reproducibility, as indicated by median coefficients of variation of 14.7% and 21.1% for protein intensities, respectively. The integrative method was found to be effective in precisely quantifying yeast proteins that were intentionally spiked in plasma at predetermined rations of 5, 2, 0.5, and 0.2 with a high genuine positive recovery with a range of 71% to 91% of all yeast proteins. The use of a complementary and finely tuned approach involving depletion and precipitation demonstrates tremendous potential in the field of discovering protein biomarkers from large-scale cohort studies. |
| HostingRepository | iProX |
| AnnounceDate | 2024-01-29 |
| AnnouncementXML | Submission_2024-01-28_20:45:26.806.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Yue Zhou |
| SpeciesList | scientific name: Homo sapiens; NCBI TaxID: 9606; |
| ModificationList | iodoacetamide derivatized residue |
| Instrument | Q Exactive HF-X |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-01-28 20:42:18 | ID requested | |
| ⏵ 1 | 2024-01-28 20:45:27 | announced |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: DIA, plasma proteomics, quantitative proteomics, depletion |
Contact List
| Feng Guan | |
|---|---|
| contact affiliation | Northwest University |
| contact email | fengguan@nwu.edu.cnm |
| lab head | |
| Yue Zhou | |
| contact affiliation | JiangNan University |
| contact email | mrriyuekong@163.com |
| dataset submitter | |
Full Dataset Link List
| iProX dataset URI |
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