Molecular Determinants Core


For more information about our services, pricing and how we can assist with your work, please call us at  443-287-7671 or contact us online.

Sample Preparation

Rigorous sample preparation is critical for successful metabolomics studies, both to protect the integrity of the biological sample as well as to achieve maximum performance of our LC-MS/MS and GC-MS/MS instrumentation.

A member of the Molecular Determinants Core team works in the lab at Johns Hopkins All Children's Hospital

The Molecular Determinants Core offers a variety of optimized protocols adapted to a wide range of samples such as biofluids (plasma, serum, urine, CSF, saliva, milk) tissues or cell cultures:

  • Automated 96-well plate-based protocols
  • Manual and supported liquid-liquid extractions
  • Tissue cryo-pulverization
A member of the Molecular Determinants Core team works in the lab at Johns Hopkins All Children's Hospital

We can also customize our protocols specifically to your samples. Please contact us early, with any questions you might have before starting a study or sample collection, so that we can provide guidance and protocols on how to best collect and preserve samples.


The Molecular Determinants Core maintains multiple cutting-edge separation and analytical platforms including multiple mass spectrometry (MS) systems coupled to gas chromatography (GC) or liquid chromatography (LC) systems.

The Molecular Determinants Core offers various targeted profiling and quantitative LC-MS/MS and GC-MS/MS analysis:

Small Molecule Metabolites (targeted profiling)

Wide range of chemical classes

  • Amino acids & derivatives including small peptides
  • Bile acids
  • Purine & Pyrimidine metabolites
  • Fatty Acids and metabolites 
  • Coenzymes & water-soluble vitamins
  • Acyl carnitines
  • Biogenic amines
  • Organic acids
  • Sugars & derivatives
  • Neurotransmitters
  • Choline & metabolites
  • Catecholamines & metabolites
  • Alkaloids & flavonoids…

Covering a wide range of biological pathways:

  • Pyrimidine & purine Biosynthesis
  • TCA Cycle
  • Pentose Phosphate Pathway 
  • Heme catabolism
  • NAD metabolism
  • Glycolysis Pathway
  • Mevalonate Pathway
  • Carnitine Biosynthesis
  • Tryptophan/Kynurenine pathway
  • Oxidative Stress Biomarkers 
  • Methionine Cycle…

Sex Hormones (quantitative)

  • Estrogens (C18 steroids)
  • Progestagens (C21 steroids)
  • Androgens (C19 steroids)

Short Chain Fatty Acids (quantitative)

  • Linear and branched fatty acids with under 6 carbons.


Data quality is critical in metabolomics. Extensive data QC analysis is performed for every project to ensure data quality and integrity.

The Molecular Determinants Core has high-throughput sample preparation capacities to process a large number of samples and increase reproducibly, and has implemented multiple normalization strategies to ensure the best quality of your data:

  • Heavy standards spiked at different stages of the process
  • QC POOL for intra and inter batch normalization
  • Osmolarity measurements for urine & saliva normalization

Data analysis

Rigorous data analysis is essential to the validity of metabolomics studies. Our team of metabolomics experts is here to help with the data processing and statistical analysis:

  • Preprocess and Normalization
  • Univariate Analysis
  • Multivariate Analysis
  • Clustering Analysis
  • Classification and Feature Selection


Correlation networks of the metabolites with significant variations with age and gender from metabolomics analysis of 200 human urine (right). Multivariate modeling of physiological variations using OPLS on the same dataset (left).  Source: Thévenot EA, Roux A, Xu Y, Ezan E, Junot C.  J Proteome Res. 2015 Aug 7;14(8):3322-35. doi: 10.1021/acs.jproteome.5b00354. Epub 2015 Jul 2.