PXD008161

PXD008161 is an original dataset announced via ProteomeXchange.

Title	Development of in planta chemical cross-linking-based quantitative interactomics in Arabidopsis
Description	An in planta chemical cross-linking-based quantitative interactomics (IPQCX-MS) workflow has been developed to investigate in vivo protein-protein interactions and alteration in protein structures in a model organism, Arabidopsis thaliana. A chemical cross-linker, azide-tag-modified disuccinimidyl pimelate (AMDSP), was directly applied onto Arabidopsis tissues. Peptides produced from protein fractions of CsCl density gradient centrifugation were dimethyl-labelled, from which the AMDSP cross-linked peptides were fractionated on chromatography, enriched, and analysed by mass spectrometry. ECL2 and SQUA-D software was used to identify and quantitate these cross-linked peptides, respectively. These computer programs integrates peptide identification with quantitation and statistical evaluation. This workflow eventually identified 354 unique cross-linked peptides, including 61 and 293 inter- and intra-protein cross-linked peptides, respectively, demonstrating that it is able to in vivo identify hundreds of cross-linked peptides at an organismal level by overcoming the difficulties caused by multiple cellular structures and complex secondary metabolites of plants. Co-immunoprecipitation and super-resolution microscopy studies have confirmed the PHB3- PHB6 protein interaction found by IPQCX-MS. The quantitative interactomics also found hormone-induced structural changes of SBPase and other proteins. This mass spectrometry-based interactomics will be useful in the study of in vivo protein-protein interaction networks in agricultural crops and plant-microbe interactions.
HostingRepository	PRIDE
AnnounceDate	2018-08-14
AnnouncementXML	Submission_2018-08-14_04:36:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fengchao Yu
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationList	monohydroxylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-11-08 00:07:53	ID requested
⏵ 1	2018-08-14 04:36:21	announced

Liu S, Yu F, Hu Q, Wang T, Yu L, Du S, Yu W, Li N, Development of in Planta Chemical Cross-Linking-Based Quantitative Interactomics in Arabidopsis. J Proteome Res, 17(9):3195-3213(2018) [pubmed]

submitter keyword: IPQCX-MS, in planta quantitative interactomics, in vivo cross-linking, ECL2, 4C proteomic workflow, Arabidopsis thaliana

Ning Li
contact affiliation	The Hong Kong University of Science and Technology
contact email	boningli@ust.hk
lab head
Fengchao Yu
contact affiliation	The Hong Kong University of Science and Technology
contact email	fyuab@connect.ust.hk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008161
     1. Label: PRIDE project
     2. Name: Development of in planta chemical cross-linking-based quantitative interactomics in Arabidopsis