Needle in a haystack

Illustration of glycoproteins present on the highly glycosylated cell surface. These proteins, often specific to diseases, can be shed or secreted into the blood stream and so are ideal targets for biomarker discovery. Credit: courtesy of Ralph Schiess and Reto Ossola, Swiss Federal Institute of Technology" />Illustration of glycoproteins present on the highly glycosylated cell surface. These

Jeffrey M. Perkel
May 1, 2008
<figcaption>Illustration of glycoproteins present on the highly glycosylated cell surface. These proteins, often specific to diseases, can be shed or secreted into the blood stream and so are ideal targets for biomarker discovery. Credit: courtesy of Ralph Schiess and Reto Ossola, Swiss Federal Institute of Technology</figcaption>
Illustration of glycoproteins present on the highly glycosylated cell surface. These proteins, often specific to diseases, can be shed or secreted into the blood stream and so are ideal targets for biomarker discovery. Credit: courtesy of Ralph Schiess and Reto Ossola, Swiss Federal Institute of Technology

Researcher:
Ruedi Aebersold, professor of molecular systems biology, Swiss Federal Institute of Technology, Zurich

Project:
Cancer biomarker discovery in serum

Problem:
If most proteins are glycosylated, most peptides are not. Thus, a whole-cell or whole-serum protein extract can overwhelm a mass spectrometer. Aebersold needed a way to focus only on glycosylated fragments.

Solution:
Aebersold enriched his samples with a method called solid-phase extraction of N-linked glycopeptides ( Nat Protocols, 2:334-9, 2007). A protein extract is digested to peptides, and treated with sodium periodate to oxidize the sugars to aldehydes....