PMC:7640975 / 14249-15886 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7640975","sourcedb":"PMC","sourceid":"7640975","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7640975","text":"The original MS/MS raw data were analyzed using the Proteome Discoverer Software 2.1 (Thermo Fisher Scientific, San Jose, CA, USA). The data were searched against the database of UniProt Sus scrofa (February 26, 2017, containing 26 103 sequences, http://www.uniprot.org/proteomes/UP000008227, version: Uniprot-proteome-UP000008227-Sus scrofa (Pig)-26103s-20170226.fasta) and porcine deltacoronavirus Uniprot database (February 26, 2017, containing 442 sequences, http://www.uniprot.org/porcinedeltacoronavirus, version: Uniprot-Porcine deltacoronavirus [1586324]-442s-20170226.fasta). The parameters for database searching were set as follows: instrument, TripleTOF 5600; cysteine alkylation, iodoacetamide; digestion, trypsin; dynamic modification, oxidation (M), acetylation (protein N-terminus), and iTRAQ8plex (Y); static modification, iTRAQ8plex (K), iTRAQ8plex (N-terminus), and carbamidomethyl (C); maximum missed cleavages, 2; precursor mass tolerance, 10 ppm; fragment mass tolerance, 0.05 Da; validation based on, q-value. To guarantee the accuracy of the MS data analysis, the cutoff value for the peptide and protein confidences was set to \u003e95% and \u003e1.20, respectively, coupled with a false discovery rate (FDR) of ≤1% for peptide and protein identifications. The t test function in the R language software was applied to calculate the p-value of the expression difference of cellular proteins between mock- and PDCoV-infected IPEC-J2 cells, and only proteins with a fold change \u003e1.20 or \u003c0.83 and a p-value \u003c 0.05, which have being widely used as the criteria for judging DEPs,28,29 were considered differentially 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