PXD024146

PXD024146 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Reliable identification of protein-protein interactions by crosslinking mass spectrometry_AP-MS
Description	Quantitative proteomics dataset on soluble, affinity-enriched proteins from SPA-pulldowns in E. coli K12, on rpoB-SPA / nusG-SPA / yacL-SPA. This data was used to identify proteins for enrichment analysis and subsequent crosslinking mass spectrometry search (DB creation). Cleared E. coli lysate was added to anti-FLAG M2 beads to isolate binders to rpoB (RNA polymerase), nusG or yacL (RNA polymerase binders. Elution was accomplished via TEV protease cleavage. A mock K12 E.coli lysate ETV elution was used to assess protein enrichment in the obtained (specific) eluates. The proteins in each fraction were precipitated using acetone, derivatized and proteolysed in-solution. Each sample was acquired as injection triplicate via LC-MS on Q Exactive HF and the raw data searched with MaxQuant with LFQ and iBAQ quantitation enabled. Further processing was done using Perseus.
HostingRepository	jPOST
AnnounceDate	2021-04-14
AnnouncementXML	Submission_2024-05-02_05:00:38.514.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ludwig Sinn
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	alpha-amino acetylated residue; L-methionine sulfoxide; S-carboxamidomethyl-L-cysteine
Instrument	instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-11 10:09:31	ID requested
1	2021-04-14 01:44:01	announced
2	2022-09-18 04:07:52	announced	2022-09-18: Updated FTP location.
⏵ 3	2024-05-02 05:00:41	announced	2024-05-02: Updated PubMed.

Publication List

Lenz S, Sinn LR, O'Reilly FJ, Fischer L, Wegner F, Rappsilber J, Reliable identification of protein-protein interactions by crosslinking mass spectrometry. Nat Commun, 12(1):3564(2021) [pubmed]

Lenz S, Sinn LR, O'Reilly FJ, Fischer L, Wegner F, Rappsilber J, Reliable identification of protein-protein interactions by crosslinking mass spectrometry. Nat Commun, 12(1):3564(2021) [pubmed]

Keyword List

submitter keyword: AP-MS, crosslinking, mass spectrometry, FDR, protein-protein interaction, E. coli

submitter keyword: AP-MS, crosslinking, mass spectrometry, FDR, protein-protein interaction, E. coli

Contact List

Prof. Dr. Juri Rappsilber
lab head
Ludwig Sinn
contact affiliation	Technische Universität Berlin, Bioanalytics, Prof. Juri Rappsilber
dataset submitter

Full Dataset Link List

jPOST dataset URI
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.jpostdb.org/JPST001090/

jPOST dataset URI

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.jpostdb.org/JPST001090/