PXD078284

PXD078284 is an original dataset announced via ProteomeXchange.

Title	Mapping Architecture of Protein complexes in Arabidopsis using XL-MS (Histone H2B turboID)
Description	Capturing molecular machines in action is key to understanding protein complex architecture, cellular regulation, and gene function. Here, we present a cross-linking mass spectrometry (XL-MS) platform using the PhoX cross-linker to map proteome-wide interactions in Arabidopsis thaliana. By analyzing whole-cell lysates, chloroplasts, and nuclei, we identified 52,944 unique cross-links pairs, corresponding to 37,531 residue pairs captured across 5,064 proteins and 3,083 protein-protein interactions (2,385 heteromeric and 698 homomultimeric). Comparison with the STRING database showed that 676 interactions had scores ≥ 0.9 and 241 ranged from 0.7–0.9. Our dataset provides residue-level interfaces that complement existing interaction networks with experimental evidence of spatial proximity. XL-MS captured the spatial organization of protein complexes, including the chloroplast 70S ribosome stalk and intermediates in photosystem repair, and revealed both shared and distinct interaction patterns across photosystems, ribosomes, and chromatin-associated proteins. The data also suggest ribosome ubiquitination, supported by diGly proteomics, and are consistent with histone interaction patterns observed using histone-TurboID. In addition, we identified an O-acyltransferase associated with histones, suggesting a potential role in chromatin-related processes. Together, these results demonstrate the utility of XL-MS for system-level mapping of the plant proteome and provide a resource for further study.
HostingRepository	PRIDE
AnnounceDate	2026-07-29
AnnouncementXML	Submission_2026-07-29_11:46:20.531.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shouling Xu
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: NEWT:3702;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2026-05-13 11:31:20	ID requested
⏵ 1	2026-07-29 11:46:21	announced

Dataset with its publication pending

submitter keyword: Cross-linking mass spectrometry (XL-MS), interlink, Arabidopsis., ribosome interactome, histone interactome,Protein-protein interaction (PPI) network, cross-links, intralink, photosystem interactome

Shouling Xu
contact affiliation	1.Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA 2.Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
contact email	sxu@carnegiescience.edu
lab head
Shouling Xu
contact affiliation	Carnegie Institution at Stanford
contact email	sxu@ciw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD078284
     1. Label: PRIDE project
     2. Name: Mapping Architecture of Protein complexes in Arabidopsis using XL-MS (Histone H2B turboID)