| Advancements in the high-throughput technologies have provided for the completion of human genome and genomes of many organisms and cell lines. However, genomic information is not sufficient enough to understand biological processes. The emergence of proteomics together with developments in mass spectrometry and bioinformatics has helped to provide a deeper understanding of the cell and its processing events. This study demonstrates how proteomic tool can be used to understand physiological changes both in Chinese hamster ovary cells as well as the fruit fly (Drosophila melanogaster) and zebra fish (Danio rerio). Since Chinese hamster ovary (CHO) cells are the preferred hosts of many recombinant proteins, it is crucial to elucidate the proteome of CHO cells for a better understanding in the development of therapeutics production. In this study, we catalogued 7,866 grouped proteins from 561,826 redundant and 88,517 unique peptides. In addition to the identification of whole secreted and intracellular proteins, 525 different N-glycosylated proteins and their N-glycosylation sites were characterized by solid phase extraction of glycosylated peptides (SPEG) coupled LC/MS/MS technique. Identification of the glycoproteome is crucial because glycosylation is associated with many cellular functions and disease states such as cancer, diabetes, neurological, neuromuscular and immunological and hereditary disorders. Zebrafish and Drosophila melanogaster are the two model animals widely used to understand the function of genes in an organism. For this reason, we identified 169 unique glycosylated proteins and their glycosylation sites of Zebrafish and 477 unique glycosylated proteins and their glycosites of Drosophila melanogaster. In order to make this huge glycoproteome data publicly available, 3 different websites, http://betenbaugh.jhu.edu/GlycoCHO/, http://betenbaugh.jhu.edu/GlycoFly/, http://betenbaugh.jhu.edu/GlycoFish/ were established. In addition, the sialylated proteome of CHO cells and Drosophila have been studied, and it is proven that Drosophila is getting sialylated. Three different proteins from cell adhesion and ion channel categories have shown to be sialylated. Furthermore, the effects of sialylation on ion channel gating and nervous system are discussed in this study. Finally, this work reviews the emerging proteomic field and how it can be used to understand the physiological processes in the complex systems, to understand the disease states, and to optimize therapeutic production. |
