AP-MS Raw data of C. burnetii-host PPIs

ABSTRACT: 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.

ORGANISM(S): Homo Sapiens

SUBMITTER: Xiaolu Xiong  

PROVIDER: PXD032380 | iProX | Fri Mar 18 00:00:00 GMT 2022

REPOSITORIES: iProX