PXD045012

PXD045012 is an original dataset announced via ProteomeXchange.

Title	Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology
Description	We developed an HX-MS2 strategy that supports the acquisition of CID-generated fragment ions alongside their peptide precursors. The approach enables true auto-validation of HX data by mining the rich set of deuterated fragments, using the extra dimension of data to simultaneously confirm the peptide ID and authenticate (even correct) MS1-based deuteration calculations. The high redundancy provided by the fragments generates an opportunity to determine the confidence of deuterium calculations using a combinatorial strategy. The approach requires DIA-based acquisition methods that are available on most MS platforms, making the switch to HX-MS2 straightforward. Considerable time is saved through auto-validation and more importantly, more complex samples can now be characterized and at higher throughput, as illustrated in a drug binding analysis of the ultralarge kinase DNA-PKcs, isolated directly from mammalian cells.
HostingRepository	PRIDE
AnnounceDate	2023-09-08
AnnouncementXML	Submission_2023-09-08_07:38:03.249.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	FrantisekFilandr
SpeciesList	scientific name: Oryctolagus cuniculus (Rabbit); NCBI TaxID: 9986; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse; Q Exactive Plus; TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-31 13:55:56	ID requested
⏵ 1	2023-09-08 07:38:03	announced

Dataset with its publication pending

submitter keyword: DIA, LC-MS, SWATH-MS, DNA-PK,HX-MS

DavidC.
contact affiliation	Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada
contact email	dschriem@ucalgary.ca
lab head
FrantisekFilandr
contact affiliation	University of Calgary
contact email	frantisek.filandr@ucalgary.ca
dataset submitter

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/2023/09/PXD045012

PRIDE project URI

• PRIDE
  1. PXD045012
     1. Label: PRIDE project
     2. Name: Automating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology