DIA-enabled discovery of alternative proteins (AltProts) in mouse heart development

In this project, we conducted an evaluation of mass spectrometry methods using mouse heart and HCT116 cell samples. The results demonstrated that the data-independent acquisition (DIA) approach outperformed data-dependent acquisition (DDA) in the identification of Altprot and canonical proteins. Subsequently, we assessed several different DIA library building methods, including traditional DDA-based library building, gas-phase fractionation(GPF) library building, and machine learning-based prediction library building. Notably, the traditional DDA library building method exhibited a higher likelihood of false positive identifications. Furthermore, we applied the aforementioned mass spectrometry methods to investigate the process of mouse heart development. Through this analysis, we identified a subset of Altprots, including ASDURF, which may potentially play crucial roles in heart development. These findings serve as a fundamental basis for future exploration and investigation of Altprot in this context.