Quantum triple quad mass spectrometer

Samples for metabolomic experiments were prepared as follows: bone tissue was cleaned of soft tissue, bone marrow, cartilage, and periosteum, then flash frozen in liquid nitrogen. Equal quantities of tissue were pulverized in liquid nitrogen and metabolites were extracted in 5 ml of 80% methanol. Extracts were dried under nitrogen stream and reconstituted in 200 μl of 50% methanol, and then analyzed using reverse phase liquid chromatography (LC) with an ion-pairing reagent in a Shimadzu HPLC coupled to a Thermo Quantum triple-quad mass spectrometer (MS). Data were analyzed using Mzrock machine learning tool kit (http://code.google.com/p/mzrock/), which automates analysis of targeted metabolomics data based on chromatographic retention time, whole molecule mass, collision energy, and resulting fragment mass. Data are presented as fold change over 3-mo-old mice. Three mice per group were analyzed.