Exploiting the proteomics revolution in biotechnology: from disease and antibody targets to optimizing bioprocess development

Abstract

Recent advancements in proteomics have enabled the generation of high-quality data sets useful for applications ranging from target and monoclonal antibody (mAB) discovery to bioprocess optimization. Comparative proteomics approaches have recently been used to identify novel disease targets in oncology and other disease conditions. Proteomics has also been applied as a new avenue for mAb discovery. Finally, CHO and Escherichia coli cells represent the dominant production hosts for biopharmaceutical development, yet the physiology of these cells types has yet to be fully established. Proteomics approaches can provide new insights into these cell types, aiding in recombinant protein production, cell growth regulation, and medium formulation. Optimization of sample preparations and protein database developments are enhancing the quantity and accuracy of proteomic results. In these ways, innovations in proteomics are enriching biotechnology and bioprocessing research across a wide spectrum of applications.

Figure 1

Overview of an optimized proteomics experiment for mammalian cell culture protein quantification. Proteins are extracted and subjected to reduction, alkylation, filter aided sample preparation, and digestion. Digested peptides are labeled with iTRAQ reagents, fractionated by bRPLC, and injected into LC/MS/MS. The resultant peaks are analyzed by mapping to CHO genome databases. Differences in peak levels represent relative protein expression levels between cell lines. Identification and quantification of proteins aids bioprocess development efforts to increase protein yields or other applications.

Figure 2

An example output for identified proteins in CHO-K1 proteome (CHO Proteome Database; URL: http://chogenome.org/proteomeSearch.php). (a) The protein name and accession number is retrieved after searching with a name. There are 6163 proteins total in this database (as shown by entering ‘%%’ for searching all the database proteins). (b) After clicking on an accession number, detailed information about a particular protein can be seen, including identified peptide sequences.