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PXD019120

PXD019120 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleReliable identification of protein-protein interactions by crosslinking mass spectrometry_CLMS_BS3&DSSO_datasets
DescriptionCrosslink 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.
HostingRepositoryjPOST
AnnounceDate2021-04-14
AnnouncementXMLSubmission_2022-09-18_03:22:58.640.xml
DigitalObjectIdentifierhttp://dx.doi.org/10.6019/PXD019120
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterLudwig Sinn
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListS-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide
Instrumentinstrument
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-05-12 04:49:03ID requested
12021-04-14 02:01:21announced
22022-09-18 03:22:59announced2022-09-18: Updated FTP location.
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: crosslinking, mass spectrometry, CLMS, FDR, protein-protein interaction, PPI, E. coli
Contact List
Prof. Dr. Juri Rappsilber
lab head
Ludwig Sinn
contact affiliationTechnische Universit├Ąt 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/