Proteomic Analysis of Chinese Hamster Ovary Cells

To complement the recent genomic sequencing of Chinese
hamster ovary (CHO) cells, proteomic analysis was performed on CHO cells
including the cellular proteome, secretome, and glycoproteome using
tandem mass spectrometry (MS/MS) of multiple fractions obtained from
gel electrophoresis, multidimensional liquid chromatography, and solid
phase extraction of glycopeptides (SPEG). From the 120 different mass
spectrometry analyses generating 682 097 MS/MS spectra, 93 548
unique peptide sequences were identified with at most 0.02 false
discovery rate (FDR). A total of 6164 grouped proteins were identified
from both glycoproteome and proteome analysis, representing an 8-fold
increase in the number of proteins currently identified in the CHO
proteome. Furthermore, this is the first proteomic study done using
the CHO genome exclusively, which provides for more accurate identification
of proteins. From this analysis, the CHO codon frequency was determined
and found to be distinct from humans, which will facilitate expression
of human proteins in CHO cells. Analysis of the combined proteomic
and mRNA data sets indicated the enrichment of a number of pathways
including protein processing and apoptosis but depletion of proteins
involved in steroid hormone and glycosphingolipid metabolism. Five-hundred
four of the detected proteins included N-acetylation
modifications, and 1292 different proteins were observed to be N-glycosylated. This first large-scale proteomic analysis
will enhance the knowledge base about CHO capabilities for recombinant
expression and provide information useful in cell engineering efforts
aimed at modifying CHO cellular functions.