PXD003658 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD003658
- Label: PRIDE project
- Name: In planta chemical crosslinking and mass spectrometry analysis of protein structure and interaction in Arabidopsis