PXD026076

PXD026076 is an original dataset announced via ProteomeXchange.

Title	Identification of ischemia-reperfusion induced protein changes in human intestine using quantitative (phospho)proteomics and MALDI mass spectrometry imaging
Description	Intestinal ischemia-reperfusion injury (IR) is a severe clinical condition, and unraveling its pathophysiology is crucial in order to improve therapeutic strategies and reduce the high morbidity and mortality rates. Here, we studied the dynamic proteome and phosphoproteome in human intestine during ischemia and reperfusion, using LC-MS analysis to gain quantitative information of thousands of proteins and phosphosites, as well as MS imaging to obtain spatial information. We identified a significant decrease in abundance of proteins related to intestinal absorption, microvillus and cell junction, whereas proteins involved in innate immunity, in particular the complement cascade, and extracellular matrix organization increased in abundance after IR. Differentially phosphorylated proteins were involved in RNA splicing events and cytoskeletal and cell junction organization. In addition, our analysis points to MAPK and CDK families to be active kinases during IR. Finally, MALDI-TOF MS imaging presented peptide alterations in abundance and distribution, which resulted, in combination with FTICR-MS imaging and LC-MS, in the identification of additional proteins related to RNA splicing, the complement cascade and extracellular matrix organization. This study expanded our understanding of the molecular changes that occur during IR in human intestine, and highlights the value of the complementary use of different MS-based methodologies.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:01:34.925.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juan Manuel Valverde
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-18 06:24:11	ID requested
1	2022-11-08 02:59:11	announced
⏵ 2	2023-11-14 08:01:37	announced	2023-11-14: Updated project metadata.

Kip AM, Valverde JM, Altelaar M, Heeren RMA, Hundscheid IHR, Dejong CHC, Olde Damink SWM, Balluff B, Lenaerts K, Combined Quantitative (Phospho)proteomics and Mass Spectrometry Imaging Reveal Temporal and Spatial Protein Changes in Human Intestinal Ischemia-Reperfusion. J Proteome Res, 21(1):49-66(2022) [pubmed]

submitter keyword: intestine, reperfusion, phosphoproteomics,ischemia

Maarten Altelaar
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, BijvoetCenter for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
contact email	m.altelaar@uu.nl
lab head
Juan Manuel Valverde
contact affiliation	Utrecht University
contact email	j.m.valverdebarrantes@uu.nl
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/2022/11/PXD026076

PRIDE project URI

• PRIDE
  1. PXD026076
     1. Label: PRIDE project
     2. Name: Identification of ischemia-reperfusion induced protein changes in human intestine using quantitative (phospho)proteomics and MALDI mass spectrometry imaging