PXD033904 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Rapid and ion mobility-resolved phosphoproteomics with dia-PASEF |
Description | Mass spectrometry-based phosphoproteomics has identified >150,000 post-translational phosphorylation sites in the human proteome. To disentangle their functional relevance, complex experimental designs that require increased throughput are now coming into focus. Here, we apply dia-PASEF on a trapped ion mobility (TIMS) mass spectrometer to analyze the phosphoproteome of a human cancer cell line in short liquid chromatography gradients. At low sample amounts equivalent to ~20 ug protein digest per analysis, we quantified over 13,000 phosphopeptides including ~8,700 class I phosphosites in one hour without a spectral library. Decreasing the gradient time to 15 min yielded virtually identical coverage of the phosphoproteome, and with 7 min gradients we still quantified about 80% of the class I sites with a median coefficient of variation <10% in quadruplicates. We attribute this in part to the increased peak capacity, which effectively compensates for the higher peptide density per time unit in shorter gradients. Our data shows a five-fold reduction in the number of co-isolated peptides with TIMS. In the most extreme case, these were positional isomers of nearby phosphosites that remained unresolved with fast chromatography. In summary, our study demonstrates how key features of dia-PASEF translate to phosphoproteomics. |
HostingRepository | PRIDE |
AnnounceDate | 2022-10-26 |
AnnouncementXML | Submission_2022-10-26_01:28:10.462.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | FlorianMeier |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | phosphorylated residue |
Instrument | timsTOF Pro |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-05-16 06:49:36 | ID requested | |
⏵ 1 | 2022-10-26 01:28:10 | announced | |
2 | 2023-11-14 08:59:05 | announced | 2023-11-14: Updated project metadata. |
Publication List
Keyword List
submitter keyword: TIMS, technology, PASEF, dia-PASEF,Phosphoproteomics, data-independent acquisition, ion mobility |
Contact List
FlorianMeier |
contact affiliation | Jena University Hospital Am Klinikum 1 07743 Jena Germany |
contact email | florian.meier@med.uni-jena.de |
lab head | |
FlorianMeier |
contact affiliation | Jena University Hospital |
contact email | florian.meier@med.uni-jena.de |
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/2022/10/PXD033904 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD033904
- Label: PRIDE project
- Name: Rapid and ion mobility-resolved phosphoproteomics with dia-PASEF