Mass spectrometry resources for visualizing cellular processes

The staff at the Stanford University Mass Spectrometry (SUMS) lab.

Photo:  Kris Newby

Behold the Waters Xevo TQ-XS Tandem Quadrupole mass spectrometer! With its state-of-the-art separations, ion sources, and detectors, you can analyze molecules in your biological specimens with amazing accuracy. And the Stanford University Mass Spectrometry (SUMS) lab is there to help.

Mass spectrometry is the workhorse technology used by scientists to understand biochemical processes, structures and inner workings of cells. SUMS maintains and operates a wide array of mass spec-related instrumentation to support researchers both inside and outside of Stanford. It is the mass spec core for Bio-X, an interdisciplinary biosciences institute that brings together biomedical and life science researchers, clinicians, engineers, physicists, and computational scientists to unlock the secrets of the human body. The lab also runs the “Proteomics Shared Resource” of the Stanford Cancer Institute.

Beyond sharing its equipment and expertise, the lab’s staff facilitates researcher education and custom methods development. Staff can help researchers with experimental design, sample preparation, data interpretation and result analysis. The lab also organizes a lunch seminar series to support the vibrant and growing mass-spec community on campus. Seed grant programs aim to mitigate risk for principle investigators, by incorporating mass spec into their research, developing new workflows and applications, and generating preliminary data for external grant proposals.

“Mass spectrometry is more useful and important than ever across a wide range of fields, including the physical and life sciences, medicine, and engineering,” said lab director Allis Chien. “SUMS and the many other shared resource labs on campus make advanced technologies accessible to researchers in all these disciplines.

SUMS’ premier annual event is its Research Applications Symposium, held this year on October 10. SUMS-RAS 2019 featured a day of mass spec-related research news, networking, sneak previews of upcoming technologies and applications. This year’s keynote speaker, Garry Nolan, PhD, professor of microbiology and immunology, wowed the crowd with his plans to build an ion-beam device that could create high resolution images at an atomic scale, creating unprecedented windows into the structures of cells, immune system behavior, and progressions of tumors.

Nolan went on to describe how using this technology could help scientists recognize the unique cellular “neighborhoods” of immune cells that form with a pathogen attack, a traumatic injury, or an autoimmune disease.

“Seeing is believing,” said Nolan, as he explained how this new visualization technology could be used to gain clinical insights into the mechanisms-of-action of anti-cancer and immune therapies.

Nolan also announced that he’d like to create a “Core” for scientists who want to use his lab’s Multiplexed Ion Beam Imaging (MIBI) systems for subcellular analysis. These systems are capable of analyzing up to 45 molecular targets simultaneously, within standard, formalin-fixed, paraffin-embedded (FFPE) tissue specimens. By marking molecules with multicolored tags, the inner workings of cells can be transformed into observable light shows, illuminating previously invisible processes, such as the way microbes invade cells or how immune system cells destroy tumors.

All of this is made possible by a generous gift from Vincent and Stella Coates, given through the Stanford School of Medicine, as well as support from Stanford Cancer Institute grant NIH P30 CA124435 and the Stanford Dean of Research.

To initiate resource use, enter your request on the iLab website. Contact SUMS at for questions, custom projects or new application development.