PXD003658

PXD003658 is an original dataset announced via ProteomeXchange.

Title	In planta chemical crosslinking and mass spectrometry analysis of protein structure and interaction in Arabidopsis
Description	Mass spectrometry analysis in combination with the site-specific chemical cross-linking has emerged as a powerful method in study of three-dimensional structure of protein complex and in mapping of protein-protein interactions (PPIs). Even though in vitro cross-linking experiments have been widely applied to investigate the specific interactions of a bait protein and its targets, the measurement of in vivo protein tertiary structure and PPIs has been problematic and strenuous due to the dynamic nature of the biological systems and a lower number of cross-linked peptides that can be isolated via MudPIT (Multidimensional Protein Identification Technology) for mass spectrometry analysis. Using Arabidopsis thaliana as a model multicellular eukaryotic organism, we have attempted to develop an improved in vivo chemical cross-linking and mass spectrometry (or IPXL-MS) workflow, which aims at optimizing the in vivo cross-linking conditions, establishing of a MudPIT procedure for enrichment of cross-linked peptides, and developing an integrated software program to identify the in planta chemical cross-linked peptides, by which three pairs of in vivo cross-linked peptides of high-confidence has been identified twice from two independent biological replicates. This work has demarked a beginning of alternative proteomic approach in study of in vivo protein tertiary structure and PPIs in higher plants. This in vivo cross-linking approach may be applied into other model multicellular organisms, such as mouse, for molecular systems biological research.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:09:09.863.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	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-02-17 03:07:12	ID requested
1	2016-06-28 07:21:47	announced
⏵ 2	2024-10-22 04:09:10	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201500310;

Zhu X, Yu F, Yang Z, Liu S, Dai C, Lu X, Liu C, Yu W, Li N, In planta chemical cross-linking and mass spectrometry analysis of protein structure and interaction in Arabidopsis. Proteomics, 16(13):1915-27(2016) [pubmed]

curator keyword: Biological

submitter keyword: Arabidopsis, mass spectrometry, disuccinimidyl suberate, in planta chemical cross-linking, interactomics, exhaustive cross-linked peptides identification tool

NIng Li
contact affiliation	Division of Life Science, The Hong Kong University of Science and Technology
contact email	boningli@ust.hk
lab head
Fengchao Yu
contact affiliation	University of Michigan
contact email	fyuab@connect.ust.hk
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/2016/06/PXD003658

PRIDE project URI

• PRIDE
  1. PXD003658
     1. Label: PRIDE project
     2. Name: In planta chemical crosslinking and mass spectrometry analysis of protein structure and interaction in Arabidopsis