PXD019797-2
PXD019797 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | A Data-independent Acquisition-based Global Phosphoproteomics System Enables Deep Profiling |
| Description | Phosphoproteomics can provide insights into cellular signaling dynamics. To achieve robust quantitative phosphoproteomics profiling from minute amounts of sample, we here develop a global phosphoproteomics strategy based on data-independent acquisition (DIA) mass spectrometry and high-quality hybrid spectral libraries derived from data-dependent acquisition (DDA) and DIA data. Benchmarking the method using 166 synthetic phosphopeptides shows high sensitivity (<0.1 ng), accurate site localization and reproducible quantification (~5% median coefficient of variation). As a proof-of-concept, we use lung cancer cell lines and patient-derived tissue to construct a hybrid phosphoproteome spectral library covering 159,524 phosphopeptides (88,107 phosphosites). Based on this library, our single-shot streamlined DIA workflow quantifies 36,350 phosphosites (19,755 class 1) in cell line samples within 2 hours. Application to drug-resistant cells and patient-derived lung cancer tissues delineates site-specific phosphorylation events associated with resistance and tumor progression, showing that our workflow enables the characterization of phosphorylation signaling with deep coverage, high sensitivity and low between-run missing values. |
| HostingRepository | jPOST |
| AnnounceDate | 2021-03-05 |
| AnnouncementXML | Submission_2022-09-18_02:41:24.227.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Reta Birhanu Kitata |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
| ModificationList | S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide; O-phospho-L-serine; O-phospho-L-threonine; O4'-phospho-L-tyrosine |
| Instrument | LTQ Orbitrap |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2020-06-15 17:45:08 | ID requested | |
| 1 | 2021-03-04 19:23:05 | announced | |
| ⏵ 2 | 2022-09-18 02:41:24 | announced | 2022-09-18: Updated FTP location. |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: phosphoproteome, data-independent acquisition, spectral library, lung cancer |
Contact List
| Yu-Ju Chen | |
|---|---|
| lab head | |
| Reta Birhanu Kitata | |
| contact affiliation | Academia Sinica |
| 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/JPST000859/ |
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