Abstract In recent years, single-cell or low-input multi-omics techniques have brought a revolution in the study of pre-implantation embryo development. However, single-cell or low-input proteome research in this field is relatively underdeveloped, due to the limited source of mammalian embryo samples, the objective reality of high abundance zona pellucida proteins, and the lack of hypersensitive proteome technology. Here, a comprehensive solution of ultrasensitive proteome technology was developed for single-cell or low-input mouse embryos. Both deep coverage route and high-throughput route could significantly reduce the starting material and enhance the proteomic depth without any customized instrument. Using the deep coverage route, an average of 2,665 or 4,585 protein groups can be identified from 1 or 20 mouse zygotes respectively. Using the high-throughput route, 300 single mouse zygotes can be analysis in 8 days with an average of 2,371 proteins identified. With its popularization, we believe researchers can choose deep coverage or high-throughput technology routes according to their own conditions.

Ultrasensitive Proteomics Depicted an In-depth Landscape for Mouse Embryo