Metabolomics Services and Assays

We offer both non-targeted and targeted analysis of small molecules by UPLC-MS, UPLC-MS/MS, and GC-MS.

Targeted small molecules analysis

Targeted profiling provides quantitative analysis of predefined analytes with known chemical structures. Absolute quantification gives results of concentrations (i.e., µg/g, µg/mL). Relative quantification gives results of peak intensities. The analysis is performed on a Waters TQ-S tandem quad mass spectrometer coupled with a Waters Classic UPLC (UPLC-MS/MS) or a Thermo GC-MS.

Our assays include phytohormone analysis, cannabinoids, amino acids, organic acids, short chain fatty acids (SCFAs), fatty acids (FAME), simple sugars, compounds involved in central carbon metabolism, etc. More details on targeted assays can be found here.

We can perform custom MRM assay development for your research needs. Contact us for further details.

Non-targeted metabolite profiling

We offer both Non-targeted metabolomics, sometimes also referred to as global profiling of metabolites, seeks to characterize all the measurable analytes in a sample as fully as possible, including chemical unknowns. Known standards for metabolites of interest can also optionally be included in non-targeted metabolomics analysis.

Our standard UPLC-MS acquisition workflow involves a reverse phase chromatographic separation, which provides efficient separation of moderately polar to nonpolar metabolites. We utilize a Waters instrumentation platform which enables operation in MS^E mode enabling the simultaneous acquisition of MS data and indiscriminant fragmentation spectra (i.e. no precursor ion selection) in alternating scans. Feature detection and alignment are performed using the open source XCMS package (1) and subsequent dataset wide correlational grouping and compound annotation is performed using in-house tools (2). Standard workflows for non-targeted metabolite profiling by GC-MS are based on the use of a TG-5MS column which provides efficient separation of both highly polar and nonpolar metabolites. Volatile metabolites are extracted by solid phase microextraction (SPME) and analyzed using GC-MS.


(1) Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G. XCMS: Processing mass spectrometry data for metabolite profiling using Nonlinear peak alignment, matching, and identification. Analytical chemistry. 2006;78(3):779-87

(2) Broeckling C, Heuberger A, Prince J, Ingelsson E, Prenni J. Assigning precursor–product ion relationships in indiscriminant MS/MS data from non-targeted metabolite profiling studies. Metabolomics. 2012:1-11