PXD019120

PXD019120 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Reliable identification of protein-protein interactions by crosslinking mass spectrometry_CLMS_BS3&DSSO_datasets
Description	Crosslink mass spectrometry dataset on soluble, SEC-fractionated high-molecular weight proteome of E. coli, crosslinked with BS3 or DSSO. This data was used to identify protein-protein interactions and to obtain information on protein (complex) topologies. In the end, the data was used for finding and evaluating a reliable approach for error control in crosslink mass spectrometry, particularly for PPI-studies. Cleared E. coli lysate was fractionated in the range of 3 MDa to 150 kDa (44 fractions). After taking aliquots for quantitative proteomics (JPST000843 ), the aliquots were split and the proteins in each fraction crosslinked (with BS3 or DSSO) and pooled again for each crosslinker set. Then, the pool was precipitated, derivatized and proteolysed in-solution. Digests were fractionated by SCX and hSAX (9x10 offline-fractionation matrix). Afterward, each peptide fraction was acquired via LC-MS on Q Exactive HF. Raw data was pre-processed (denoising, peak-list generation, error correction) and this data searched with xiSEARCH 1.6.746 using differing databases. FDR was calculated using xiFDR (version 2.0dev) under various settings to probe several FDR approaches.
HostingRepository	jPOST
AnnounceDate	2021-04-14
AnnouncementXML	Submission_2024-05-02_05:01:02.340.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD019120
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Ludwig Sinn
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrument	instrument

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2020-05-12 04:49:03	ID requested
1	2021-04-14 02:01:21	announced
2	2022-09-18 03:22:59	announced	2022-09-18: Updated FTP location.
⏵ 3	2024-05-02 05:01:03	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: crosslinking, mass spectrometry, CLMS, FDR, protein-protein interaction, PPI, E. coli

submitter keyword: crosslinking, mass spectrometry, CLMS, FDR, protein-protein interaction, PPI, 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/JPST000845/

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/JPST000845/