Metabolomics / Biomarker discovery

Biomarker / Untargeted platform

We perform untargeted biomarker research using a high resolution Q-TOF (AB-Sciex 5600 Triple TOF MS) to monitor and compare thousands of analytes from biological samples. Compounds of interest from statistical analysis are identified using either database matching of MS/MS patterns, comparison to standards, or de-novo identification using ultra-high resolution analysis (Orbitrap Fusion, Thermo-Fisher Scientific)

Quantitative / Targeted metabolomics panels

We measure several hundreds of metabolites using absolute quantification, utilizing stable isotope dilution, 6-8 pt standard curves and 4 levels of QC analysis within each batch.  Most quantitative assays are run on a triple quadrupole LC-MS/MS system (API-4500, AB Sciex).  Panels include:

 

 

 

 

 

 

 

Intracellular energy metabolite panel: Primary metabolites and cofactors associated with energy production in the cell.  Absolute quantification of nucleotides (e.g. ATP, ADP, AMP, GTP, GDP,...etc), sugar phosphates (glycolysis, pentose phosphate intermediates), coenzymes/cofactors (e.g. NADH, NAD+, acetyl-CoA, etc).  This platform uses either cell culture or tissue as the matrix for analysis (compound list).

 

 

 

 

 

 

 

 

 

 

 

 

 

Lipidomics Panel:  Phospholipids, fatty acids (un-, polyunsaturated), eicosanoids, acylcarnitines, and bile acids.  Relative quantification of a variety of hydrophobic metabolite classes critical for metabolism, modulating inflammation, and signaling. Peaks are normalized to appropriate stable isotope internal standards for ideal inter-sample comparisons. Method was developed for plasma and serum samples, but is adaptable to all types of biological tissues that contain measurable levels of these metabolites (compound list). Lipid compound list can be customized for individual projects.

Global metabolite panel: (ideal for plasma, serum, urine, or even cells).  These several hundred metabolites are found both intra- and extracellularly and include amino acids, organic acids, acylcarnitines, purines and pyrimidines, bile acids and more.  These compounds are quantified within two separate runs to cover multiple ionization modes.  This panel may be measured in conjuction with the UCSD Biochemical Genetics Lab (www.ucsdbglab.org)

Nearly 40 compounds quantified in single run, with a stable isotope included for each compound

Resolution of each phosphorylation state

ensures no interferences in metabolite quantitation

Statistical analysis

Both univariate and multivariate statistical analysis are performed.  Multivariate analysis can include either unsupervised (PCA) or supervised (PLS-DA) analysis, with the goal of creating a model that characterizes a particular cohort by a metabolic signature. Pathway enrichment analysis can also be performed to identify particular pathways of interest from a dataset.  Univariate analysis (e.g. T-test or ANOVA analysis) will be done to identify key fold changes with statistical significance.

Collaboration with proteomics core at University of California-San Diego

If you are interested in quantitative proteomics analysis of the same sample from which metabolite profiling is performed, we have optimized a single extraction procedure to analyze both from the same sample.  This work is done in collaboration with the Biomolecular proteomic facility at UCSD, directed by Majid Ghassemian. PhD.  We will perform the initial extraction, run the metabolomics experiments, and coordinate the proteomic analysis with Dr. Ghassemian, who will analyze the protein pellet of the extraction. We will provide a single full report at the conclusion of both experiments. Specific types of proteomic services can be found at: http://bpmsf.ucsd.edu/protein-based-analysis/protein-quantification/index.html

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