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 <i>UBE3A </i>knockout and isogenic control neurons differentiated for 21 days in neuronal culture conditions. Three independent replicates of <i>UBE3A </i>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.