Metabolomics Services and Assays

We offer both non-targeted and targeted analysis of smalle molecules by both UPLC-MS and GC-MS. Please see our page on instrumentation for current capabilities.

Non-targeted metabolite profiling:

UPLC-MS: Our standard UPLC-MS acquisition workflow involves a reverse phase chromatographic separation (C8 or C18 column) 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).

GC-MS: 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.

Targeted metabolite analysis:

UPLC-MS: Targeted analysis is performed on a Waters TQ-S tandem quad mass spectrometer coupled with caplillary scale UPLC. We can performed custom MRM assay development for your research needs.

Standard assays availble:

  • steroids (testosterone, progesterone, dihydrotestosterone, cortisol, and cortisone)
  • plant hormones (abscisic acid, dihydrophaseic acid, and phaseic acid)

GC-MS: Targeted analysis is performed using selection ion monitoring (SIM). Custom assay development is available.

Standard assays available:

  • short chain fatty acids
  • amino acids
  • mono- and disaccharides
  • lipids/fatty acids
  • small phenolics
  • sterols



(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

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Fort Collins, Colorado 80523
Maintained by Jessica Prenni