Research Group Lab Hall

Medical College of Wisconsin Shared Mass Spectrometry (MSMS) Facility - Small Molecules

The MSMS Facility is an interdepartmental research service unit managed on behalf of the Medical College of Wisconsin by the Department of Pharmacology and Toxicology. It provides service and consultation for research projects requiring mass spectrometric analysis. Three mass spectrometers are available to analyze samples. We operate on a fee for service basis.


The facility provides quantitation using SRM (MRM) for known compounds. In addition, the facility can identify unknown small molecules using MS/MS techniques. The facility will implement reported procedures for analysis and quantitation and will develop new methods that answer specific investigator-driven questions. Typical analyses carried out by the laboratory are listed below. Examples are shown in other tabs.
  • Complex lipids - oxylipins like the eicosanoids, glycerophospholipids, sphingolipids, gangliosides, S1P, triglycerides, cholesteryl esters, and adrenal steroids.
  • Smaller, volatile lipids - cholesterol, oxysterols, fatty acids.
  • Endocannabinoids - palmitoylethanolamide, N-arachidonoylethanolamine (anandamide), 2-arachidonoylglycerol, and similar molecules.
  • Drugs of abuse - THC and its metabolites, other drugs can be measured.
  • Metabolites - tryptophan metabolites, TMAO, etc.
  • Peptides - angiotensin and its metabolites, other bioactive peptides, synthetic peptides.

Analysis can be simple or complex. Using lipidomic analysis as an example, analysis may only involve total phospholipid quantitation. However, more in-depth analysis of molecular species and FA composition of the molecular species can be performed on glycerophospholipids.

Agilent 6460 Triple Quadrupole LC Mass Spectrometer 

agilent 6460

 The 6460 Triple Quad LC/MS/MS has a Jet Stream ionization source interfaced to a model1290 Infinity liquid chromatograph and autosampler. The mass analyzer has an upper range of 3000 m/z in both positive and negative detection modes and a data-sampling rate of 150 SRMs per second. The 6460 routinely achieves fmol sensitivity and it is suitable for the qualitative and quantitative determinations of many types of small molecules.

Thermo Scientific Triple Quadrupole-GC Mass Spectrometer 

thermoscientific tsq 8000

The TSQ 8000 mass spectrometer (GC/MS/MS) is equipped for electron impact (EI) and chemical ionization (CI) with the capability of performing CID experiments. The analyzer has a mass range up to 1100 m/z in both positive, negative and pulsed positive-negative detection modes. It is interfaced to a Trace 1310 gas chromatograph equipped with a cooled TriPlus autosampler. 

Guidelines for Mass Spectrometry Services

  1. Please visit our iLab page to request services.
  2. Facility personnel are available to meet and discuss the possibility of utilizing the mass spectrometry for your research projects.
  3. When it is possible please find protocols for sample preparation and experimental design. We will provide some suggestions if needed.
  4. A request form (PDF) must be completed explaining the sample type, number of samples, length of project, sample purity, estimated concentration range, what type of analysis, etc.
  5. The cost of the analyses will be covered by fee-for-service. If column is needed that is not already in the facility then the user may be required to purchase the column. The cost of internal standards will be charged in full if the facility does not feel that other users will need a similar assay. When extensive development time is required the user is expected to pay these costs.
  6. You will be charged for all samples and standards analyzed.
  7. If you have no current funding, you may request assistance in obtaining preliminary data for your proposal. If needed, the facility will provide a brief protocol of the MS analysis for your proposal and assist you with budget information for MS analysis.

Current Pricing

  • Charge per sample: $11/each
  • MS run time: $42/hour
  • Sample workup and/or setup: $42/hour
  • Data analysis and report: $42/hour
  • Supplies (nozzles/tips): $2/each
  • Administrative costs: $8/billing

MSMS Contact Us

Basic Science Building, Room 624-626

Michael J. Thomas, PhD

(414) 955-8605

Rachel Kallinger

(414) 955-8610