Easy numbers

User:
Catherine Fenselau, professor of chemistry and biochemistry, University of Maryland, College Park

Project:
Identifying molecular mechanisms of drug resistance in breast cancer

Problem:
Fenselau works with several drug-resistant and drug-sensitive cell lines, and she wanted a cheap and simple way to compare protein abundance among them.

Solution:
Fenselau's approach, proteolytic ¹⁸O labeling, is simplicity itself. "It works, we know how to do it, and it's less expensive than other methods, especially metabolic labeling," she says. Two protein extracts are digested to peptides, one in normal ¹⁶O water, and the other in labeled ¹⁸O water. Each peptide produces two peaks differing in mass by 4 Daltons (because two water molecules are used in the cleavage reaction); the ratio of peaks reveals how the peptide's abundance in one sample compares with the other.

Fenselau uses cultured cells, but the technique works equally well with tissue samples. It also labels every peptide ...