PXD006707 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Mass spectrometric analysis of membrane protein topology |
Description | Here we made an attempt to obtain partial structural information on the topology of multispan integral membrane proteins of yeast by isolating organellar membranes, removing peripheral membrane proteins at pH 11.5 and introducing chemical crosslinks between vicinal amino acids either using homo- or hetero-bifunctional crosslinkers. Proteins were digested with specific proteases and the products analysed by mass spectrometry. Dedicated software tools were used together with filtering steps optimized to remove false positive crosslinks. In proteins of known structure, crosslinks were found only between loops residing on the same side of the membrane. As may be expected, crosslinks were mainly found in very abundant proteins. Our approach seems to hold to promise to yield low resolution topological information for naturally very abundant or strongly overexpressed proteins with relatively little effort. |
HostingRepository | PRIDE |
AnnounceDate | 2017-10-11 |
AnnouncementXML | Submission_2017-11-08_04:32:53.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Mykhaylo Debelyy |
SpeciesList | scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; |
ModificationList | iodoacetic acid derivatized residue; iodoacetamide derivatized residue |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2017-06-13 23:39:57 | ID requested | |
1 | 2017-10-11 08:48:45 | announced | |
⏵ 2 | 2017-11-08 04:32:54 | announced | Updated publication reference for PubMed record(s): 29073188. |
Publication List
Debelyy MO, Waridel P, Quadroni M, Schneiter R, Conzelmann A, Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins. PLoS One, 12(10):e0186840(2017) [pubmed] |
Keyword List
curator keyword: Biological |
submitter keyword: BS3, EDC, multispan proteins, transmembrane domains, pLink |
Contact List
Andreas Conzelmann |
contact affiliation | Division of Biochemistry, Department of Biology, University of Fribourg, Fribourg, Switzerland |
contact email | andreas.conzelmann@unifr.ch |
lab head | |
Mykhaylo Debelyy |
contact affiliation | Lab.: 0.313; Division of Biochemistry, Department of Biology, Faculty of Science, University of Fribourg, Chemin du Musée 10, CH-1700, Fribourg, Switzerland; Tel.: +41263008660 |
contact email | mykhaylo.debelyy@unifr.ch |
dataset submitter | |
Full Dataset Link List
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/2017/10/PXD006707 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD006707
- Label: PRIDE project
- Name: Mass spectrometric analysis of membrane protein topology