PXD033904

PXD033904 is an original dataset announced via ProteomeXchange.

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	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:59:04.575.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Florian Meier
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	timsTOF Pro

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.

Dataset with its publication pending

submitter keyword: TIMS, technology, PASEF, dia-PASEF,Phosphoproteomics, data-independent acquisition, ion mobility

Florian Meier
contact affiliation	Jena University Hospital Am Klinikum 1 07743 Jena Germany
contact email	florian.meier@med.uni-jena.de
lab head
Florian Meier
contact affiliation	Jena University Hospital
contact email	florian.meier@med.uni-jena.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD033904
     1. Label: PRIDE project
     2. Name: Rapid and ion mobility-resolved phosphoproteomics with dia-PASEF