PXD066803

PXD066803 is an original dataset announced via ProteomeXchange.

Title	Mapping Hydrogen Migration Barriers for Site-Specific HDX-MS
Description	A longstanding limitation of Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) has been the inability to directly measure amide exchange with single amide resolution. Excitation of peptides either during ionization, ion transmission, or collision induced dissociation rapidly induces intermolecular hydrogen migration, leading to a loss of the native-deuterium labeled state of the peptide; a term commonly known as ‘scrambling’. Electron-based fragmentation methods in conjunction with gentle ion transmission settings can minimize scrambling, but often not completely. Scrambling has been shown to vary with ion transmission settings, peptide charge, and size, but the properties that govern the energetic barriers of scrambling within peptides are not well understood. Furthermore, it remains unclear whether scrambling is generally a global process, or if local scrambling networks commonly exist within peptides. Here we examine a panel of peptides using gentle electron transfer dissociation and map the energetic barriers of scrambling to define a relationship between peptide charge density and scrambling propensity. This study suggests that by and large, the scrambling process has a single energetic barrier and involves all exchangeable sites within a peptide. For some peptides the barrier of scrambling is surprisingly close to the barrier of amide bond dissociation.
HostingRepository	PRIDE
AnnounceDate	2025-10-14
AnnouncementXML	Submission_2025-10-14_13:53:42.883.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Charles Mundorff
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Equus caballus (Horse); NCBI TaxID: NEWT:9796; scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Ascend

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-31 07:07:37	ID requested
⏵ 1	2025-10-14 13:53:43	announced

10.1016/J.MCPRO.2025.101075;

ProteomeXchange project tag: Hydrogen Deuterium Exchange (HDX-MS)

submitter keyword: ETD, HDX-MS, Scrambling

Miklos Guttman
contact affiliation	University of Washington, School of Pharmacy, Department of Medicinal Chemistry
contact email	mguttman@uw.edu
lab head
Charles Mundorff
contact affiliation	University of Washington
contact email	mundorff@uw.edu
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/2025/10/PXD066803

PRIDE project URI

• PRIDE
  1. PXD066803
     1. Label: PRIDE project
     2. Name: Mapping Hydrogen Migration Barriers for Site-Specific HDX-MS