and Mass Spectrometry

Services: Targeted Metabolomics
Sample Preparation

     There are three common ways to prepare a sample for metabolic profiling, depending on the matrix:

  1. Plasma and/or serum samples. These samples are extracted with 4x volume ice cold methanol, spun at 13,200 rpm to pellet insoluble proteins and larger lipids, evaporated to dryness and reconstituted in 90% H2O/10% ACN /0.1% formic acid for HPLC-MS analysis.

  2. Cerebrospinal fluid samples. Given the more hydrophobic character of these compounds, these samples are extracted in 4x volume 50/50 Methyl tert-butyl ether and 1-chlorobutane. They are centrifuged at 3000 rpm for ten minutes, with the organic layer being harvested. This is evaporated to dryness and reconstituted in methanol for HPLC-MS analysis.

  3. Urine. These samples are treated with a solid phase extraction method prior to HPLC-MS analysis.


     Please schedule an appointment with Bill Webb to discuss preparation methods for your individual experiments.


Sample Preparation. Comparison of features shared in between metabolite extraction methods, the dendrogram was produced by applying a clustering algorithm to show similarities between the methods. Within the constraints established by the dendrogram, the table is sorted by the number of reproducible features, this produced four groups, I, II, III and IV. The diagonal shaded boxes contain the total number of reproducible features for each method, defined as a feature that was detected in at least 5 out of 6 LC/MS runs for a given extraction method. The remaining boxes contain the number of identical features shown as a pair-wise comparison between methods. Abbreviations: methanol (MeOH), ethanol (EtOH), acetonitrile (ACN), sulfosalicylic acid (SSA), trichloroacetic acid (TCA), perchloric acid (PCA).