Tandem mass spectrometry and bioinformatics analysis

The mass spectrometry characterization of the BPLF1 interactome was previously reported [²⁴]. For the current analysis, proteins that were absent in duplicate samples of immunoprecipitates from cells transfected with the FLAG-empty vector but were detected by at least one unique spectral count in both the FLAG-BPLF1 and FLAG-BPLF1[C61A] immunoprecipitates were considered as positive hits. The bioinformatics resource DAVID [⁵⁸] was used to identify the overrepresentation of genes in particular functional categories. Pathways databases including Gene Ontology [^59,60], Panther [⁶¹] and the Kyoto Encyclopedia of Genes and Genomes (KEGG) [⁶²] were used for functional annotation. Functional interaction network analysis was performed using the Search Tool for the Retrieval of Interacting Genes (STRING) database v. 9.0 [⁶³]. STRING integrates information on physical interactions and functional relationships identified by high-throughput biochemical analysis, mining of databases and literature, and prediction from genomic context analysis, into Protein-Protein-Interaction (PPI) networks.