A mouse model of Fragile X Syndrome analyzed by quantitative proteomics: a comparison of methods

We have compared the performance of seven different strategies in the analysis of a mouse model of Fragile X Syndrome, involving the knockout of the fmr1 gene that is the leading cause of autism spectrum disorder. Focusing on the cerebellum, we show that Data-Independent Acquisition (DIA) and the TMT-based Real-time Search method (RTS) generated the most informative profiles, generating 334 and 329 significantly altered proteins respectively, although the latter still suffered from ratio compression. Label-free methods such as BoxCar and a conventional Data-Dependent Acquisition were too noisy to generate a reliable profile, while TMT methods that do not invoke RTS showed a suppressed dynamic range. The TMT method based on complementary ions (ProC) overcomes ratio compression, but current limitations in ion detection reduces sensitivity. Overall, both DIA and RTS uncovered known regulators of the syndrome and detected alterations in calcium signalling pathways that are consistent with calcium deregulation recently observed in imaging studies.