Innovating mass spectrometry to drive biological discovery and advance human health.

Coon Laboratories

Our laboratory develops and applies mass spectrometric technology to study human health. We use these tools to answer fundamental questions in cell biology and to study human diseases including Alzheimer’s, diabetes, heart failure, cancer, obesity, asthma, among several others. The research team currently consists of twelve Ph.D. students, two postdoctoral fellows, two undergraduate researchers, and six staff scientists.


Our mission is to facilitate expedient, comprehensive analysis of biological molecules to advance biomedical research.

Untangling the multi-faceted networks that regulate complex organisms and their diseases will require innovative technologies to globally monitor many classes of biomolecules, including lipids, proteins, and metabolites. We aim to fill this technology gap by developing innovative mass spectrometry-based technologies.


The Coon Group’s most valuable resource is its collection of driven, energetic, and passionate researchers.

Scientists in the Coon Laboratory have diverse backgrounds and skill-sets making our group a veritable melting pot of ideas.  Students and staff work together in small teams tackling exciting projects ranging from building new mass spectrometry instrumentation to analyzing the proteomes of human tissue specimens.


Occupying newly renovated space within the Genome Center of Wisconsin, we are nestled between Chemistry, Biochemistry, Genetics, Biomolecular Chemistry, and the Wisconsin Institutes for Discovery.

Our state-of-the-art laboratory houses approximately one dozen mass spectrometers, each equipped with gas or liquid chromatographs.  We have a variety of hybrid mass spectrometer instrument configurations including quadrupole, quadrupole linear ion trap, and Orbitrap mass analyzers.  This array of heavy mass spec artillery is complemented by more conventional laboratory instrumentation including plate readers, automated liquid handling robots, balances, centrifuges, etc.


Our laboratory is equipped with a dozen state-of-the-art hybrid mass spectrometers.  With these systems, and close connections to our industrial partners, we innovate tomorrow’s mass spectrometry technology.

We are fortunate to house and operate the latest in high resolution, high performance mass spectrometer technology – including several of the latest generation Orbitrap systems. We have a long running collaboration with Thermo Fisher Scientific, the world’s leading MS manufacturer, and through these interactions have complete access to modify and develop on these fully functional MS platforms.  We work closely with the UW’s patent foundation (WARF) to transfer our new technologies to industrial partners for commercialization. Since 2006, WARF has filed dozens of patent applications based upon our inventions, leading to several commercial products. Many of the technologies currently under development have the similar promise to impact hundreds of laboratories worldwide to solve countless biomedical questions.

May 10, 2021 in News

Congratulations to new graduate Justin McKetney

Congratulations to Justin McKetney, the Coon lab’s newest PhD graduate. Justin and Prof Joshua Coon…

Read More
April 9, 2021 in News

Qiuwen Quan Earns Biochem Award

Congratulations to Coon lab member Qiuwen Quan who was selected to receive a 2021 Biochemistry…

Read More
March 17, 2021 in News

Muehlbauer explores adding FAIMS to the phosphoproteomic workflow

Mass spectrometry is the premier tool for identifying and quantifying protein phosphorylation on a global…

Read More
November 4, 2020 in Articles, News

Peters-Clarke explores efficient and effective peptide fragmentation in tandem MS

Photoactivation and photodissociation are useful tools in tandem mass spectrometry, but implementation often involves cumbersome…

Read More
July 24, 2018 in Articles, Featured, News

Nicholas Riley Featured in Badger Chemistry News

Nicholas Riley was featured in Badger Chemistry News! Read the interview here:

Read More
June 9, 2018 in Articles, Featured, News

Paul Hutchins Manuscript Recently Published in Cell Systems

Paul Hutchins manuscript, LipiDex: an integrated software package for high-confidence lipid identification, received numerous positive…

Read More

Y3K Project

The Yeast 3 Thousand (Y3K) dataset comprises over 1000 proteomes, 1000 lipidomes, and 1000 metabolomes, profiled with an aim of better understanding mitochondrial biology.

Learn more about the Y3K Project by reading the article in the November 2016 issue of Nature Biotechnology or from our Y3K website on the link below.

Coon Group Alumni

Even beyond the impact of our science, the most important product of our research is a rapidly growing cohort of alumni who are now engaged in the biomedical enterprise in various academic and industrial settings.

Earn your Ph.D. with us

The Coon Group is always on the lookout for new members.  Professor Coon accepts students from several UW-Madison doctoral programs including Chemistry, the Integrated Program in Biochemistry (IPiB), and Cellular & Molecular Pathology.