PXD035362

PXD035362 is an original dataset announced via ProteomeXchange.

Title	Dataset 3 from 'Protein complexes in Bacillus subtilis by AI-assisted structural proteomics'
Description	We 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.
HostingRepository	jPOST
AnnounceDate	2023-01-31
AnnouncementXML	Submission_2023-01-31_07:30:12.408.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Francis O'Reilly
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationList	L-methionine sulfoxide; S-carboxamidoethyl-L-cysteine; L-glutamic acid 5-methyl ester (Glu); deamidated L-asparagine; unknown modification; unknown modification
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-07-17 12:11:05	ID requested
⏵ 1	2023-01-31 07:30:12	announced

Dataset with its publication pending

submitter keyword: Crosslinking mass spectrometry, DSSO, Bacillus subtilis

Juri Rappsilber
lab head
Francis O'Reilly
contact affiliation	NCI-NIH
dataset submitter

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/JPST001791/