Mass spec is a qualitative technique, not a quantitative one. Unless you take some extra steps, the heights of all those mass spectral peaks scattered across the pages of the biological literature do not reflect protein amounts.
That's because the two techniques most often used to inject biological samples into a mass spectrometer – matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization – can play molecular favorites, says Catherine Fenselau, professor of chemistry and biochemistry at the University of Maryland. "Ions are formed by adding or removing a proton, and empirically, you don't get the same signal response for the same amounts of different samples," she explains. "So the peak height or volume is not necessarily representative of the starting amount."
That means that two different compounds present in equal amounts might produce different peak heights in isolation. Adding to the confusion, compounds in mixtures can compete for ionization, skewing results even more, says Michael Gross, professor of chemistry at Washington University in St. Louis and editor of the Journal of the American Society for Mass Spectrometry.
Researchers have developed a number of ways to make this qualitative technique quantitative. But which to choose? The Scientist asked mass spec experts to walk you through the pros and cons of their preferred methods.
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