Shared Resources News

The Flow Cytometry core is excited to share that the new BD FACSDiscover A8 is now available at the Thomas Lab.

Get real-time single cell imaging, every event gets an in-focus brightfield & fluorescence image with no sacrifice in acquisition speed. Diffusivity, symmetry, and other morphology metrics gate directly in FACSChorus alongside your fluorescence data. The BD Spectral FX full-spectrum detection has 5-laser configuration with up to 78 fluorescence detectors resolves 50+ parameters per cell. 

Equipment Highlights 

• High Speed - 35,000 events/sec

• Imaging Mode – 12,500 events/sec

• 8 scatter and imaging detectors

• Sheath-free water fluidics 

Join us for a lunch-and-learn and an analysis seminar to learn more about this new equipment! Details below in Upcoming Events section. 

Awardee: Phil Corrin SR Contributors: Leslie Hermosillo, Jake Kennedy, Alex Zevin 

Supporting Faculty Labs: Kevin Cheung, Guang-Shing Cheng

Genomics now supports the Olink Reveal Proteomics Assay. The Genomics and Bioinformatics Shared Resource now offers the Olink Proximity Extension Assay. This high-throughput method allows users to measure more than 1,000 proteins in serum and plasma and upwards of 5,000 proteins in tissue and cells.  Why are the Genomics and Bioinformatics SR supporting a Proteomics Assay?!?

The Olink Reveal assay complements standard mass spectrometry-based proteomics approaches by enabling high-throughput profiling of a defined set of protein targets and is compatible with complex biological matrices that can be otherwise challenging for mass spectrometry, such as plasma and serum. (end italics here) This Olink technology uses oligonucleotide-conjugated antibodies to detect specific target proteins in a standard 96-well plate. After the antibodies bind to their target proteins, the oligonucleotide tags are amplified and sequenced on an Illumina NextSeq 2000 or NovaSeq X Plus. Olink’s analysis software can then read the resulting sequence data and translate that into normalized protein counts. This assay will support teams in biomarker discovery and translational research examining protein changes associated with disease, treatment, or other biological conditions. 

With funding provided by the Shared Resources Assay/Model/Technology Grant, the Genomics and Bioinformatics Shared Resource and Proteomics and Metabolomics Shared Resource collaborated to pilot and validate an automated method to process Olink Reveal assay plates. Our pilot study demonstrated concordance with mass spectrometry results as well as with Olink assay results generated by a third-party vendor. We have begun processing samples for researchers. 

We are excited to be able to provide this high-throughput proteomics technology to Fred Hutch and Cancer Consortium researchers. Contact us at genomics@fredhutch.org to schedule your project.

August 2026

With a great deal of gratitude to our partners in Philanthropy, Shared Resources has recently introduced the Orbitrap Astral Zoom Mass Spectrometer in Proteomics and the Lunaphone Comet in Experimental Histopathology.  These two new state-of-the-art systems will advance your research to the moon and back!

Astral Zoom

The Fred Hutch Proteomics & Metabolomics Shared Resource has acquired a new state-of-the-art mass spectrometer, the Thermo Fisher Scientific Orbitrap Astral Zoom, to expand support for proteomics research. The instrument combines three mass analyzers: a quadrupole for ion isolation, an Orbitrap for high-resolution and accurate mass measurements, and the novel Astral analyzer, which delivers exceptional sensitivity and high dynamic range at acquisition rates of up to 270 Hz. Together with an upgraded instrument architecture, these technologies provide a next-generation platform for both high-sensitivity and high-throughput proteomics.

Compared with current instrumentation operating at 45 Hz, which supports whole-proteome analysis of highly fractionated samples at a rate of approximately six samples per day, the Astral Zoom enables whole-proteome analysis from a single 200 ng injection at up to 24 samples per day, with additional throughput gains anticipated through ongoing optimization. Initial testing has demonstrated deep proteome coverage of more than 9,500 proteins in human samples, excellent quantitative precision (average %CV <10%), and approximately 50% fewer missing values than the Shared Resource's existing mass spectrometers.

The Astral Zoom's enhanced sensitivity enables researchers to explore previously inaccessible regions of the proteome, while its increased throughput lowers the cost per sample, making large-scale proteomics studies more financially feasible and allowing complex projects to be completed more quickly.

To learn more about how this new capability can support your research, please contact the Proteomics & Metabolomics Shared Resource.

Lunaphore Comet

Thanks to a generous philanthropic donation, Experimental Histopathology is excited to now offer a new advancement in Space-tial Biology with multiplex IF (mIF) staining on the Lunaphore COMET instrument! The Lunaphore COMET is an automated staining and digital imaging platform, enabling detection of up to 40 unique protein and/or RNA markers on the same tissue section, with flexibility in panel design and 20X fluorescent imaging for single-cell resolution.  Customized panels can be developed using your favorite IHC-compatible antibodies and up to 12 RNAscope probes.  The final OME-TIFF file for each slide is compatible with a variety of image analysis software to allow researchers to choose the best option for their needs.  Contact us at exphisto@fredhutch.org to discuss how the COMET can take your research to the stars!

August 2026

A multidisciplinary collaboration between Comparative Pathology, Proteomics, Experimental Histopathology, Cellular Imaging and Genomics, the Shared Resources Assay/Model/Technology (AMT) Development award for “Enumeration and laser capture of lung cancer metastasis in a mouse model using AI workflows” was recently completed.

This project served to improve manual pathology and spatial proteomics workflows by

1. utilizing a pathologist-informed AI-based classifier to detect lung tumor metastases from scanned H&E images using HALO AI (Figure 1) and
2. incorporating automated protein extraction, laser capture microdissection (LCM) collection, and AI-directed LCM into the mass spectrometry (MS)-based spatial proteomics workflow (Figure 2).

Replacing manual dissection with automated tools optimized efficiency, increased precision and reproducibility in the LCM and proteomic workflow, resulting in higher throughput and more efficient use of limited specimens. Importantly, the HALO classifier is adaptable to user-generated data across tumor models, and the resulting digital image-to-proteomics workflow provides a fast, scalable, and cost-effective platform for spatial discovery at an estimated cost of $156–$327 per ROI, depending on scale.

Compared with current image-based spatial technologies, which are generally limited to fewer than 100 protein targets, laser capture microdissection (LCM)-based proteomic workflows provide cost-efficient, high-fidelity profiling of hundreds of proteins, enabling deeper biological insight without the significant expense of large-scale spatial studies.

More information: Save the Date! We will be presenting more on this project at the Shared Resources Lunchtime Seminar Wednesday, December 16 11:30-12:30 pm, Thomas D1-080/084 Sze. Please contact Raisa Glabman with any questions.

August 2026

Shared Resources hosts a monthly lunchtime seminar series, complete with food.  Please join us to hear from scientists across the consortium whose work was made possible by the experts and equipment in Shared Resources.  This newsletter will include a recap of the most recent presentation along with the schedule for future presentations.  These seminars are an excellent time to join the SR community in asking questions and learning more about real-life examples of how SR can collaborate in supporting you.

 August brought us the Genomics Shared Resource hosted seminar From Sample to Insight: Automated Workflows Powering Cancer & Vaccine Discovery, presented by  Beckman Coulter’s Genomics, Automation and Cell Health teams and Dr. Gabe Boyle, a postdoctoral researcher at Seattle Children’s Research Institute in Dr. Jay Sarthy’s lab. In his seminar entitled Chromatin Profiling Reveals CBFA2T3::GLIS2 Hijacks mSWI/SNF Complexes to Drive High-Risk Pediatric Leukemia Gabe provided an overview of his work on chromatin regulation in CBFA2T3::GLIS2 fusion-driven acute myeloid leukemia, a rare and extremely deadly pediatric leukemia that lacks effective targeted treatments. His work leveraged the Fred Hutch's Genomics SR’s, led by Dr. Alex Zevin, high-throughput AutoCUT&RUN/AutoCUT&Tag platform to identify which genes the fusion gene aberrantly activates to drive oncogenesis. Integrating chromatin profiling with immunoprecipitation mass spectrometry, he and his team discovered that CBFA2T3::GLIS2 hijacks mSWI/SNF chromatin remodeling complexes to rewire cells. From these insights, we identified new potential chemotherapeutic treatment options for children with this devastating disease.