Chinese hamster ovary (CHO) cells have been the predominant host for recombinant protein production over the past decades with major efforts directed towards cell line engineering to increase amount and quality of biopharmaceutics. Emerging omics approaches and corresponding techniques now allow an extensive characterization of cellular expression systems. Technical improvements in sequencing, mass spectrometry techniques and focusing on defined cellular subsystems unraveled new possibilities for knowledge-based CHO engineering. We found that spotlighting a defined subset of molecules with certain properties or localization, called sub-omics, can provide a better understanding of the respective cellular subsets, enabling the identification of new engineering targets. In this review, we provide an overview of how recent advances from cellular sub-transcriptomes, sub-proteomes and the secretome analyses were and can be utilized for cell line development.