PXD031926

PXD031926 is an original dataset announced via ProteomeXchange.

Title	Top-down detection of oxidative protein footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation and Electron-Capture Dissociation
Description	Fast photochemical oxidation of proteins (FPOP) footprinting is a structural mass spectrometry method that maps proteins by fast and irreversible chemical reactions. The position of oxidative modification reflects solvent accessibility and site reactivity and thus provides information about protein conformation, structural dynamics, and interactions. Bottom-up mass spectrometry is an established standard method to analyze FPOP samples. In the bottom-up approach, all forms of the protein are digested together by a protease of choice, which results in mixture of peptides from various subpopulations of proteins with varying degrees of photochemical oxidation. But, once the protein is already oxidized at least once, the spatial distribution of any consecutive oxidation no longer truly reflects initial protein solvent accessibility and residue reactivity, because the site preference of further oxidation may also be influenced by the changes caused by the prior oxidation. Thus, it would be interesting to obtain an assessment of the protein structure based on the FPOP data, by analyzing only singly oxidized protein populations. This requires utilization of more specific top-down mass spectrometry approaches. The key element of any top-down experiment is selection of a suitable method of ion isolation, excitation and fragmentation. Here we employ and compare collision-induced dissociation (CID), electron-transfer dissociation (ETD), and electron-capture dissociation (ECD) combined with multi continuous accumulation of selected ions (CASI). Singly oxidized subpopulation of FPOP labeled ubiquitin was used to optimize the method. The usefulness was then demonstrated further by using it to visualize structural changes induced by cofactor removal from holo/apo myoglobin system. The top-down data were compared with the literature and with the bottom-up data set obtained on the same samples. The top-down results were found to be in a good agreement, which indicates that monitoring singly FPOP oxidized ion population by top-down is a functional workflow for oxidative protein footprinting.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:02:38.780.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zdenek Kukacka
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	monohydroxylated residue
Instrument	Bruker Daltonics solarix series

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-28 02:56:01	ID requested
1	2023-07-20 10:49:45	announced
⏵ 2	2023-11-14 09:02:40	announced	2023-11-14: Updated project metadata.

Yassaghi G, Kuka, č, ka Z, Fiala J, Kavan D, Halada P, Voln, ý M, Nov, á, k P, Top-Down Detection of Oxidative Protein Footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation, and Electron-Capture Dissociation. Anal Chem, 94(28):9993-10002(2022) [pubmed]

submitter keyword: electron-transfer dissociation,Fast photochemical oxidation of proteins, top-down, collision-induced dissociation, mass spectrometry., electron-capture dissociation

Petr Novak
contact affiliation	Institute of Microbiology, The Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic,
contact email	pnovak@biomed.cas.cz
lab head
Zdenek Kukacka
contact affiliation	Institute of Microbiology, The Czech Academy of Sciences
contact email	zdenek.kukacka@biomed.cas.cz
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/2023/07/PXD031926

PRIDE project URI

• PRIDE
  1. PXD031926
     1. Label: PRIDE project
     2. Name: Top-down detection of oxidative protein footprinting by Collision-Induced Dissociation, Electron-Transfer Dissociation and Electron-Capture Dissociation