Johns Hopkins All Children's Hospital

Sample preparation guidelines

Extensive sample preparation is necessary for successful metabolomics studies that begins at the time of sample collection.  These efforts are necessary both to protect the integrity of the biological sample as well as to achieve maximum performance of the LC-MS/MS instrumentation.


Quenching is necessary to prevent enzymatic degradation of the metabolites in the sample.  A few options are an acid or methanol quench, or at a minimum keeping the sample on ice to at least slow metabolic changes.


There is a difference between profiling studies versus quantitative studies.  For relative quant, internal standards (heavy isotopes) are not necessary, but for absolute quantitation, HIS standards are necessary.  These should be introduced at the sample preparation stage, as an estimator of extraction efficiency.

Study Size

The CRIB’s current capacity is best suited to analysis of discovery cohorts, that is a limited number of samples and controls that allow researchers to develop and refine their hypotheses for the planning of a full-scale research study.  Acceptance of larger studies depends upon instrument and staff availability and will be considered by the CRIB advisory board on a case-by-case basis. An n of 6 is recommended as a minimum group size for a study.

Please contact us with any questions you might have before starting a study or sample collection, if possible, and we will be happy to provide guidance and protocols on how to best collect and preserve samples.