PXD032380

PXD032380 is an original dataset announced via ProteomeXchange.

Title	AP-MS Raw data of C. burnetii-host PPIs
Description	Fifty-three Coxiella effectors were expressed in HEK-293T cells, and the Strep-tagged Coxiella effectors and the corresponding interacting complex were purified for MS analysis. The LC-MS/MS analyses were performed with an Orbitrap Fusion Tribrid mass spectrometer (Thermo Fisher Scientific) coupled online to a nanoflow LC system (EASY-nLC 1000 or 1200, Thermo Fisher Scientific). The MS data acquired were searched against the Uniprot Swiss-Prot Human database with the addition of C. burnetii proteins by Proteome Discoverer software (version 2.4, Thermo Fisher Scientific, Bremen, Germany). Only the two biological replicates with the closest protein numbers and the highest PCC were retained for interaction identification. The negative controls, which consisted of only 200-600 proteins, were discarded altogether. Instead, we downloaded the contaminant repository of all 28 groups of HEK293T cells from the CRAPome, and took the two with the highest spectral count as negative controls, to obtain the high-confidence interactions. Finally, 53 effectors and 2 control was used for SAINTexpress analysis with the cut-off BFDR<0.01. The top 5th percentiles proteins ranked by occurrence rate in CRAPome all human data (443 genes) were removed from pathogen-host interactions identified by SAINTexpress.
HostingRepository	iProX
AnnounceDate	2022-03-18
AnnouncementXML	Submission_2022-09-29_23:43:16.536.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mengjiao Fu
SpeciesList	scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-03-17 18:54:08	ID requested
1	2022-03-17 18:54:29	announced
⏵ 2	2022-09-29 23:43:17	announced	2022-09-30: Update publication information.

Fu M, Liu Y, Wang G, Wang P, Zhang J, Chen C, Zhao M, Zhang S, Jiao J, Ouyang X, Yu Y, Wen B, He C, Wang J, Zhou D, Xiong X, A protein-protein interaction map reveals that the Coxiella burnetii effector CirB inhibits host proteasome activity. PLoS Pathog, 18(7):e1010660(2022) [pubmed]

submitter keyword: AP-MS, C. burnetii, PPIs

Xiaolu Xiong
contact affiliation	Beijing Institute of Microbiology and Epidemiology
contact email	xiongxiaolu624@163.com
lab head
Mengjiao Fu
contact affiliation	Beijing Institute of Microbiology and Epidemiology
contact email	1308907329@qq.com
dataset submitter

iProX dataset URI