1. Institute for Systems Biology, Seattle, Washington, USA; 2. Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
*To whom correspondence should be addressed:
The Institute for Systems Biology, 401 N. Terry, Seattle, WA 98109-5234, USA, Tel.: 206-732-1201 (LH), Fax: 206-732-1299, E-mail: lhood@systemsbiology.org; or Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada, Tel.: 778-782-9097 (BS), Fax: 778-782-3765, E-mail: bingyun_sun@sfu.ca
E14.Tg2a mouse embryonic stem (mES) cells are a widely used host in gene trap and gene targeting techniques. Molecular characterization of host cells will provide background information for a better understanding of functions of the knockout genes. Using a highly selective glycopeptide-capture approach but ordinary liquid chromatography coupled with mass spectrometry (LC-MS), we characterized the N-glycoproteins of E14.Tg2a cells and analyzed the close relationship between the obtained N-glycoproteome and cell-surface proteomes. Our results provide a global view of cell surface-protein molecular properties, in which receptors seem to be much more diverse but lower in abundance than transporters on average. In addition, our results provide a systematic view of the E14.Tg2a N-glycosylation, from which we discovered some striking patterns, including an evolutionarily preserved and maybe functionally selected complementarity between N-glycosylation and the transmembrane structure in protein sequences. We also observed an environmentally influenced N-glycosylation pattern among glycoenzymes and extracellular matrix proteins. We hope that the acquired information enhances our molecular understanding of mES E14.Tg2a as well as the biological roles played by N-glycosylation in cell biology in general.