Fig. 3

LC–MS/MS identifies TBX2 interaction partner in E14.5 lungs. a Diagram depicting the strategy to identify TBX2 interacting proteins in embryonic lungs. Tissue of E14.5 wildtype formaldehyde fixed lungs was homogenized, cells were lysed, and nuclei extracted. Protein complexes containing TBX2 were purified with an α-TBX2 antibody. Subsequent LC–MS/MS analysis and statistical filtering (Student's t-test difference of ≥ 2) revealed an enrichment of 219 proteins within the α-TBX2 fraction compared to the control lacking the α-TBX2 antibody. Manual exclusion of mitochondrial, proteasomal, and ribosomal proteins as well as hemoglobins, immunoglobins and non-nuclear proteins lead to a list of 119 candidate proteins. Of these, 22 were associated with the GO term “transcriptional regulation”, 7 with the terms “histone/histone modification”. 7 proteins were in the intersection of both GO term lists. b, c List of enriched proteins associated with the GO term “transcription regulation” (b) and “histones” or “histone modification” (c) according to DAVID functional analysis. d STRING analysis of interactions of the candidate proteins shown in (b) and (c). Three clusters were identified using MCL clustering with an inflation parameter of 2, an interaction score of high confidence (0.700) and deactivating the interaction source "textmining"