PXD034639 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | An improved TurboID-based proximity labeling pipeline in C. elegans by biochemical depletion of endogenously biotinylated carboxylases |
Description | To review an improved proximity-labeling strategy that uses the improved E. coli biotin ligase TurboID to characterize C. elegans protein complexes, the interactome of a presynaptic active zone protein, ELKS-1, was analyzed as proof of principle. A significant constraint on the sensitivity of TurboID-based proximity labeling is the presence of abundant, endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a co-factor. We developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry, by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography (IMAC). |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:56:43.683.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | WeiQiang Chen |
SpeciesList | scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; |
ModificationList | biotinylated residue; acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-06-19 04:46:00 | ID requested | |
1 | 2022-09-12 11:47:11 | announced | |
⏵ 2 | 2023-11-14 08:56:44 | announced | 2023-11-14: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: synapse, IMAC, APEX2, proximity-dependent protein labeling, HRP, biotinylated carboxylase depletion,TurboID, Caenorhabditis elegans |
Contact List
Mario de Bono |
contact affiliation | Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria |
contact email | mdebono@ista.ac.at |
lab head | |
WeiQiang Chen |
contact affiliation | Mass Spectrometry Facility, Max Perutz Laboratories Support GmbH |
contact email | chenweiqiang@gmail.com |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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[ - ]
- PRIDE
- PXD034639
- Label: PRIDE project
- Name: An improved TurboID-based proximity labeling pipeline in C. elegans by biochemical depletion of endogenously biotinylated carboxylases