User:
Ruedi Aebersold, professor for molecular systems biology, Swiss Federal Institute of Technology, Zurich
Project:
Breast cancer biomarker discovery in human serum
Problem:
Aebersold needed a technique that could look for differentially expressed proteins in hundreds of clinical samples.
Solution:
Aebersold favors a label-free approach, in which tryptic digests of cytosolic or nuclear proteins from hundreds of cell lines and tissue samples representing the disease state are fractionated by highly reproducible liquid chromatography (LC) before mass spec analysis is done. The technical combination provides three-dimensional "feature maps" (chromatographic retention time vs. mass vs. abundance), which may be computationally mined to identify peptides whose abundance correlates with disease state.
Because the approach requires no extra reagents, it's easy to incorporate many samples into the analysis (required for biomarker discovery) and add new ones as they arise. With techniques such as iTRAQ, by contrast, "you have to know a priori you want ...
