PXD056754-1
PXD056754 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Differences of uniquely identified peptides between ddaPASEF and diaPASEF |
| Description | Recent advancements in mass spectrometry-based proteomics have made it possible to conduct comprehensive protein analysis. In particular, the emergence of the data-independent acquisition (DIA) method powered by machine learning has significantly improved protein identification effi-ciency. However, compared with the conventional data-dependent acquisition (DDA) method, the degree to which peptides are uniquely identified by DIA and DDA has not been thoroughly ex-amined. In this study, we identified over 10,000 proteins using the DDA and DIA methods and analyzed the characteristics of unique peptides identified by each method. Results showed that the number of peptides uniquely identified by DDA and DIA was 19% and 32%, respectively, with shorter peptides preferentially detected by the DIA method. In addition, more DIA-specific peptides were identified, especially during the first 10% of elution, and the overall 1/K0 and m/z shifted to-ward smaller values than in the DDA method. In addition, comparing the phosphorylation and ubiquitination proteome profiles with those of whole-cell lysates by DDA showed that the en-richment of post-translationally modified peptides resulted in wider m/z and 1/K0 ranges. Notably, the ubiquitin peptide-enriched samples displayed a broader range of 1/K0 at lower m/z values than the phosphoproteome. These findings suggest a bias in the types of peptides identified by the ac-quisition method and the importance of setting appropriate ranges for DIA based on the post-translational modification of peptide characteristics. |
| HostingRepository | jPOST |
| AnnounceDate | 2024-12-01 |
| AnnouncementXML | Submission_2024-11-30_07:00:04.661.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Iwasaki Mio |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
| ModificationList | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; Acetyl; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine; ubiquitinylated lysine |
| Instrument | instrument; instrument |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2024-10-12 07:28:25 | ID requested | |
| ⏵ 1 | 2024-11-30 07:00:05 | announced | |
| 2 | 2024-12-19 21:40:08 | announced | 2024-12-20: Updated PubMed. |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: ddaPASEF, diaPASEF |
Contact List
| Mio Iwasaki | |
|---|---|
| lab head | |
| Iwasaki Mio | |
| contact affiliation | Kyoto University |
| dataset submitter | |
Full Dataset Link List
| jPOST 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://ftp.jpostdb.org/JPST003416/ |
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