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PXD003658

PXD003658 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIn planta chemical crosslinking and mass spectrometry analysis of protein structure and interaction in Arabidopsis
DescriptionMass 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:09:09.863.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterFengchao Yu
SpeciesList scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationListiodoacetamide derivatized residue
InstrumentLTQ Orbitrap Velos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-02-17 03:07:12ID requested
12016-06-28 07:21:47announced
22024-10-22 04:09:10announced2024-10-22: Updated project metadata.
Publication List
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]
Keyword List
curator keyword: Biological
submitter keyword: Arabidopsis, mass spectrometry, disuccinimidyl suberate, in planta chemical cross-linking, interactomics, exhaustive cross-linked peptides identification tool
Contact List
NIng Li
contact affiliationDivision of Life Science, The Hong Kong University of Science and Technology
contact emailboningli@ust.hk
lab head
Fengchao Yu
contact affiliationUniversity of Michigan
contact emailfyuab@connect.ust.hk
dataset submitter
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Dataset FTP location
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PRIDE project URI
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