Biochemistry Mass Spectrometry

The MCW MS Center is being restructured.   The Thermo LTQ Orbitrap Velos (Watson) and the Thermo Orbitrap Fusion Lumos (Porter) will be part of the Translational Metabolomics Shared Resource core effecitve July 1st. Please reach out to Michaela Pereckas ( for information about using those resources in the new core. The Thermo LTQ instrument will still be available for walk up service through this core. Please contact Austin Schoen ( for more information.

Overview of the MS Center

The Center for Biomedical Mass Spectrometry Research (MS Center), founded in 2017 at the Medical College of Wisconsin (MCW), integrates state-of-the-art instrumentation, bioinformatics, and scientists with expertise in mass spectrometry to support a wide range of study designs through collaborative interactions. In some cases, we can assist investigators complete simple projects using predefined fee-for-service workflows.This unique collaborative model enables us to offer a broader range of customized analysis types beyond what you might find in a typical “core” facility.

Overall, we actively promote basic and translational research programs across nearly every basic science and clinical department at MCW. Beyond catalyzing interdisciplinary research, we are also committed to fostering technology development and providing education regarding the applications of mass spectrometry in biomedical research.  

Example Services

Targeted metabolomics assays provide relative quantitation of steady state levels of metabolites and small molecules. We can develop custom assays for molecules not included in our established assays and for this purpose have an in-house compound library of 650 molecules to start from, when appropriate. Investigator prepares samples via approved SOP provided by MS Center. Investigator provides purified compound for method development.

Established Assay #1: 

Established Assay #2: 

Quantitative proteomics by peptide quantitation enables comparison of relative protein abundances across experimental conditions. Our technologies support both untargeted and targeted analyses. While not an all-inclusive list, several of the most common study types are untargeted, label-free; untargeted, TMT labeled; and targeted. The MS Center will perform all sample prepareation steps from protein digestion to clean up. 

Proximity proteomics is used to identify protein-protein interactions. While not an all-inclusive list, several of the most common study types are BioID APEX, and epitope tags.


Porter: Thermo Orbitrap Fusion Llumos

Watson: Thermo LTQ Orbitrap Velos

Hendrix: Thermo LTQ***

Ellington: Agilent 6430 QqQ



***Self-Service. We offer training workshops for our self-service instruments that include didactic lectures and hands-on exercises. For self-service users, these are the first step in receiving training to operate the instrumentation independently.



Michaela Pereckas
Research Associate, Center for Biomedical Mass Spectrometry Research


The Center is located in the modern Translational and Biomedical Research Center (TBRC) Building which is connected via skywalk to the Basic Science and Medical Education Buildings. Altogether, the Center is less than a five minute walk from most MCW research laboratories.

  • TBRC C2705: This room has dedicated space for self-service users to prepare their samples with MS-grade reagents and consumables.
  • TBRC C0825: This room is our main location, housing the majority of our instrumentation and the sample preparation area for MS Center personnel.

Our Consultation Office is located in the Basic Science Building, BSB 376D.

Links and Resources

MS Center Email:

To schedule a consultation, which is the first step in starting a project at the MS Center, please e-mail the center.



Name Role Phone Email Location
Michaela Pereckas
Research Associate
(414) 955-2837
TBRC 0825