MS identifies CDK9 as a unique binding partner for mLST8, sharing common signaling pathways and associated proteins. (A) mLST8 was immunoprecipitated from U937 cell lysates using magnetic beads preconjugated with an anti-mLST8 antibody. U937 cells were also fractionated into cytoplasmic (CYTO) and nuclear (NUC) extracts; then CDK9 was immunoprecipitated with magnetic beads preconjugated with an anti-CDK9 antibody. Rabbit IgG (RIgG) preconjugated beads were used as negative controls for nonspecific binding. Immunoprecipitated proteins were resolved by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE), and the gel was cut into 10 equivalent bands prior to standard in-gel digestion. Samples were prepared using standard techniques and then analyzed via nano LC-MS/MS. The results from MS were annotated using Metascape. The heat map shows the most significant pathways and the overlap between the 3 groups mLST8 IP, CDK9 CYTO IP, and CDK9 NUC IP. A full summary of the results is included in supplemental Table 1. (B) List of proteins from the MS results that overlap between the CDK9 IPs and mLST8 IPs. (C) The list of genes in panel B was annotated and analyzed for the most significant pathways represented using Metascape. The heat map shows the most significant pathways represented in the list of overlapping proteins. rRNA, ribosomal RNA.