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Label-free

User: Ruedi Aebersold, professor for molecular systems biology, Swiss Federal Institute of Technology, Zurich Project: Breast cancer biomarker discovery in human serum Related Articles Peak Addition Tips for Quantifying Mass Spec Easy numbers Clean targeting Multiplex counts Metabolic power Problem: Aebersold needed a technique that could look for differentially expressed proteins in hundreds of clinical samples.

Jeffrey M. Perkel

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...

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