PXD011931 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | PhoX - An IMAC-enrichable Crosslinking Reagent |
Description | Chemical crosslinking mass spectrometry is rapidly emerging as a prominent technique to study protein structures. Structural information is obtained by covalently connecting peptides in close proximity by small reagents and identifying the resulting peptide pairs by mass spectrometry. However, sub-stoichiometric reaction efficiencies render routine detection of crosslinked peptides problematic. Here we present a new tri-functional crosslinking reagent, termed PhoX, which is decorated with a stable phosphonic acid handle. This makes the crosslinked peptides amenable to the well-established IMAC enrichment. The handle allows for 300x enrichment efficiency and 97% specificity, dramatically reducing measurement time and improving data quality. We exemplify the approach on various model proteins and protein complexes, e.g. resulting in a structural model of LRP1/RAP complex. PhoX is also applicable to whole cell lysates. When focusing the database search on ribosomal proteins, our first attempt resulted in 355 crosslinks, out-performing current efforts in less measurement time. |
HostingRepository | PRIDE |
AnnounceDate | 2019-09-13 |
AnnouncementXML | Submission_2019-10-25_05:22:37.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Richard Scheltema |
SpeciesList | scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap Elite |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-12-04 07:13:06 | ID requested | |
1 | 2019-09-13 09:46:48 | announced | |
⏵ 2 | 2019-10-25 05:22:39 | announced | 2019-10-25: Updated publication reference for PubMed record(s): 31572778. |
3 | 2023-05-15 02:18:16 | announced | 2023-05-15: Updated project metadata. |
4 | 2023-05-15 02:19:21 | announced | 2023-05-15: Updated project metadata. |
Publication List
Steigenberger B, Pieters RJ, Heck AJR, Scheltema RA, PhoX: An IMAC-Enrichable Cross-Linking Reagent. ACS Cent Sci, 5(9):1514-1522(2019) [pubmed] |
Keyword List
submitter keyword: Tri-functional crosslinker, IMAC enrichable crosslinker, phosphonic acid, XlinkX, crosslinking mass spectrometry, structural biology |
Contact List
Richard Scheltema |
contact affiliation | Biomolecular Mass Spectrometry Pharmaceutical Sciences Utrecht University |
contact email | r.a.scheltema@uu.nl |
lab head | |
Richard Scheltema |
contact affiliation | Utrecht University |
contact email | r.a.scheltema@uu.nl |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD011931
- Label: PRIDE project
- Name: PhoX - An IMAC-enrichable Crosslinking Reagent