LC-MS/MS screen of day 21 cortical neurons differentiated from <i>UBE3A</i> knockout and <i>UBE3A </i>wild-type isogenic control human induced pluripotent stem cells

We used tandem mass tag (TMT) labeling to profile whole-cell lysates from UBE3A knockout and isogenic control neurons differentiated for 21 days in neuronal culture conditions. Three independent replicates of UBE3A knockout and control cultures were lysed in urea lysis buffer, digested in trypsin, each lysate was labeled with a unique isobaric tandem mass tag (TMT), and the samples combined for analysis by analyzed by liquid chromatography with tandem mass spectrometry (LC-MS/MS). LC-MS/MS analysis identified a total of 5,621 proteins of which 5,590 were detected in all 6 samples. MaxQuant software (version 1.6.14.0.) was used to normalize protein signals per sample and generate relative protein abundances (expressed as fold-change in the KO from the control) and student’s t-tests used to determine significant differences.