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PXD035362

PXD035362 is an original dataset announced via ProteomeXchange.

Dataset Summary
Title Dataset 3 from 'Protein complexes in Bacillus subtilis by AI-assisted structural proteomics'
DescriptionWe generated a whole cell interaction network using crosslinking mass spectrometry. We crosslinked B. subtilis cells in suspension with the membrane permeable crosslinker DSSO, which can be cleaved in the mass spectrometer to aid identification of the crosslinking peptides (Kao et al. 2011; Kolbowski et al. 2021). To crudely simplify the proteome prior to tryptic digestion, we lysed the crosslinked cells and separated the soluble proteome (Dataset 1), and the cell debris (Dataset 2) (see Fig. S1a and methods). These two samples were digested, crosslinked peptides were enriched and fractionated by cation exchange and then all fractions were further separated by size exclusion chromatography. To further increase the depth of analysis, we also separated the soluble proteome further by size exclusion chromatography to produce 9 pools that were each analyzed separately (Dataset 3) (Fig. S1A and methods). A 2% protein-protein interaction false discovery rate (PPI-FDR) was imposed on each of the datasets and together 560 protein interactions are reported at a combined FDR of 2.5% (with a 5% residue pair-level FDR (Lenz et al. 2020)) (Supplementary Table 1). These 560 protein interactions are underpinned by 1268 unique residue pairs.
HostingRepositoryjPOST
AnnounceDate2023-01-31
AnnouncementXMLSubmission_2023-01-31_07:30:12.408.xml
DigitalObjectIdentifier
ReviewLevelNon peer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterFrancis O'Reilly
SpeciesList scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationListL-methionine sulfoxide; S-carboxamidoethyl-L-cysteine; L-glutamic acid 5-methyl ester (Glu); deamidated L-asparagine; unknown modification; unknown modification
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-07-17 12:11:05ID requested
12023-01-31 07:30:12announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: Crosslinking mass spectrometry, DSSO, Bacillus subtilis
Contact List
Juri Rappsilber
lab head
Francis O'Reilly
contact affiliationNCI-NIH
dataset submitter
Full Dataset Link List
jPOST dataset URI
Dataset FTP location
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