Trent Peters-Clarke

Summer Undergraduate Research Experience | HHMI The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.

Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows

Check out our review on DNA-scaffolded catalysis! This link provides free full text access until the end of 2025: authors.elsevier.com/a/1m43W9CpcY.... Big thanks to co-authors @edwardpimentel.bsky.social , Ashley Ogorek, @ethan-hartman-125.bsky.social , and Caleb Cox

New TMT Tribrid from Thermo for #ASMS2026 (public info)
- IRMPD is the new UPVD
- IRMPD with TMT boosts reporter intensity by up to 240% without affecting quant
- New resolutions -> Down to 1k res, with an associated loss of signal, but at least it looks faster!
- Improved proton transfer reaction

Division of Analytical Chemistry Awards Visit the post for more.

The Field and Franklin Award for Mass Spectrometry is back! Since 1985, this award has recognize outstanding achievement in the development or application of #massspec #teammassspec. Please submit nominations by November 14! Nomination details: acsanalytical.org/awards-resou...

Hijacking Extracellular Targeted Protein Degrader–Drug Conjugates for Enhanced Drug Delivery Antibody-based therapeutics encompass diverse modalities for targeting tumor cells. Among these, antibody–drug conjugates (ADCs) and extracellular targeted protein degradation (eTPD) specifically depe...

Hijacking Extracellular Targeted Protein Degrader-Drug Conjugates for Enhanced Drug Delivery | JACS
@jacs.acspublications.org @ucsfcancer.bsky.social @jimwellsucsf.bsky.social
pubs.acs.org/doi/10.1021/...

Our manuscript describing @riley-research.bsky.social's GlyCounter informatics tool is now in press at Molecular and Cellular Proteomics. Congrats to first-author Katie Kothlow, her first first-author paper!

The manuscript is available here: www.mcponline.org/article/S153...

β-Amyloid induces microglial expression of GPC4 and APOE leading to increased neuronal tau pathology and toxicity - Molecular Neurodegeneration To define how Aβ pathology alters microglia function in Alzheimer’s disease, we profiled the microglia surfaceome following treatment with Aβ fibrils. Our findings reveal that Aβ-associated human micr...

Our new paper is out! Amyloid plaques switch on microglial GPC4, increasing neuronal tau uptake & toxicity—defining an amyloid→glia→tau pathway & a potential drug target. Pleasure to work with our collaborator @jcoutinhobudd.bsky.social. doi.org/10.1186/s130...

#Alzheimers #Glia #Tau #Amyloid

A cytokine receptor-targeting chimera (kineTAC) toolbox for expanding extracellular targeted protein degradation. Extracellular targeted protein degradation (eTPD) is as an important new modality for manipulating the extracellular proteome. However, most eTPD receptors are expressed broadly or are restricted to t...

New preprint from stellar UCSF grad student Kaan Kumru and @jimwellsucsf.bsky.social!

A cytokine receptor-targeting chimera (kineTAC) toolbox for expanding extracellular targeted protein degradation | bioRxiv
www.biorxiv.org/content/10.1...

Opinion | America First? Not When It Comes to Your Health.

"The ideas and technologies that are being destroyed today, ... some of them irreversibly, those are the cures that would have been present 20 years from now."
"It’s people who will get cancer in 10, 20, or 30 years who will really pay the price for these cuts."

www.nytimes.com/2025/08/24/o...

Excited to share our new preprint, which was years in the making! chemrxiv.org/engage/chemr...
New reactions are typically developed by trial and error. How can we speed up this process? Read on to learn how we used DNA scaffolding to perform >500,000 parallel reactions on attomole scale.
1/n

White text over a black background; “Give Cancer Hell” An OHSU Knight Cancer Institute logo is placed below.

The top text reads: Cancer is the biggest fight in the history of the world. We will win. It will be hard. We're built for it. We care. Every breath. Of every second. Of every day. Great things come from the most unexpected places. Look around. We're surrounded by heroes. This is not a job. This is our life. Cancer does not discriminate. Neither will we. Bold moves only. Cancer doesn't see us coming. We will outlast, and we will outwit it. This fight is and always will be personal. "GIVE CANCER HELL." in bold at the bottom.

Phil and Penny Knight announced today a record-breaking $2 billion gift to the Oregon Health & Science University’s Knight Cancer Institute to transform the future of cancer care and set a new standard globally.

Thank you to Phil and Penny Knight for their incredible generosity.

#GiveCancerHell

Position-specific frequency matrices can be used to calculate z-scores comparing enzyme-treated and control samples. The z-scores are plotted as heatmaps that represent an enzyme specificity profile.

New preprint: we developed a method that uses phosphoproteome-derived peptide libraries (PhosPropels) for deep specificity profiling of phosphatases and phospholyases www.biorxiv.org/content/10.1...

Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein and peptide C termini Nature Chemistry - In living systems, ATP provides an energetic driving force for protein synthesis and modification. Now, an engineered enzymatic tool has been developed for high-yield, ATP-driven...

Excited to share our latest: we engineered the reactivity of a bacterial E1-like enzyme for ATP-driven modification of C termini. Our tool mimics the logic of peptide bond formation in biology for precision modification of proteins in vitro. 🧪https://rdcu.be/ewN7C

Conventional proteomics searches struggle with many modifications and fully open searches may be difficult to interpret. We introduce a "detailed" mass offset search in #MSFragger boosting interpretability and localization especially in complex cases (e.g. FPOP data): www.biorxiv.org/content/10.1...

SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics Achieving high throughput remains a challenge in MS-based proteomics for large-scale applications. We introduce SynchroSep-MS, a novel method for parallelized, label-free proteome analysis that leverages the rapid acquisition speed of modern mass spectrometers. This approach employs multiple liquid chromatography columns, each with an independent sample, simultaneously introduced into a single mass spectrometer inlet. A precisely controlled retention time offset between sample injections creates distinct elution profiles, facilitating unambiguous analyte assignment. We modified the DIA-NN workflow to effectively process these unique parallelized data, accounting for retention time offsets. Using a dual-column setup with mouse brain peptides, SynchroSep-MS detected approximately 16,700 unique protein groups, nearly doubling the peptide information obtained from a conventional single proteome analysis. The method demonstrated excellent precision and reproducibility (median protein %RSDs less than 4%) and high quantitative linearity (median R2 greater than 0.96) with minimal matrix interference. SynchroSep-MS represents a new paradigm for data collection and the first example of label-free multiplexed proteome analysis via parallel LC separations, offering a direct strategy to accelerate throughput for demanding applications such as large-scale clinical cohorts and single-cell analyses without compromising peak capacity or causing ionization suppression.

Check out our new manuscript on parallel LC separations! Super cool how the very high scan rates of modern MS systems coupled with DIA can allow us to run several samples at the same time with little loss in depth. Congrats to Noah and the team. #JASMS pubs.acs.org/doi/10.1021/...

Feeling incredibly grateful to have received an NOA from the NIH National Cancer Institute to fund my F32 postdoctoral fellowship!

Excited to continue exploring.

#NIH #NCI #F32 #postdoc #cancerresearch

Bill Rutter passed away at age 97 yesterday. He chaired our Department through the 1970s and was instrumental in the development of UCSF basic science. He hired Christine Guthrie, Keith Yamamoto, Bruce Alberts, Marc Kirschner, Pat O’Farrell, Peter Walter, Ira Herskowitz among others.

Officially tenured. Thank you to all the mentors who guided me, and to the trainees who made this possible with your ideas, hard work, and scientific joy.

Thio-NHS esters are non-innocent protein acylating reagents - Nature Communications N-Hydroxysuccinimide (NHS)-ester derivatives are one of the most widely used acylating agents. In this work, the authors report that ring-opening reaction of the succinimide to afford N-succinamide de...

www.nature.com/articles/s41...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

If you asked me 5 years ago if it would be possible to use a de novo tool on DIA data, I would have thought it would only exist in science fiction. Love being proved wrong. Great work from Justin Sanders. #proteomics #massspectrometry
www.nature.com/articles/s41...

Huge congratulations to @chrismcgann.bsky.social who passed his PhD dissertation defense yesterday with flying colors!!

Dr. McGann was the lab’s first PhD student and now first graduate! So excited and proud of all of the things he’s accomplished!

Alan Marshall: A scientist and a Gentleman - MagLab Meet one of the greatest innovators in the history of mass spectrometry, hard at work.

RIP Alan Marshall, one of the greatest mass spectrometrists ever, and a great human to boot.

nationalmaglab.org/careers/meet...

Low-density lipoprotein receptor-targeting chimeras for membrane protein degradation and enhanced drug delivery Antibody-based therapeutics encompass diverse modalities for targeting tumor cells. Among these, antibody-drug conjugates (ADCs) and extracellular targeted protein degradation (eTPD) specifically depe...

Check out this new work from Fangzhu Zhao with @jimwellsucsf.bsky.social presenting new modalities for targeted membrane protein degradation (LIPTACs) and drug-degrader conjugates (DDCs)!
www.biorxiv.org/content/10.1...
@ucsfcancer.bsky.social @ucsfhealth.bsky.social @ucberkeleyofficial.bsky.social

Trent standing beside his poster presentation with two ASMS attendees, pointing toward the poster.

Five current or former UW-Madison Chemists reuniting at lunch in Baltimore.

A portrait of former president Barack Obama at the National Portrait Gallery.

A portrait of four women Supreme Court Justices at the National Portrait Gallery.

I had a blast last week attending my first ASMS as a postdoc!

I feel so fortunate for this mass spec community as we champion open and accessible science.

We are excited to introduce ‘time’ as a new domain for proteomics multiplexing!

It enables:
-Label-free multiplexing
-Combinatorial multiplexing with plexDIA

Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀

The #TeamMassSpec world has seen exciting instrumentation advances in the past few years that have changed how we interrogate the proteome.

We reviewed modern MS instrument platforms and the acquisition strategies they enable.

Now available on #ChemRxiv: doi.org/10.26434/che...

Integrating Alternative Fragmentation Techniques into Standard LC-MS Workflows Using a Single Deep Learning Model Enhances Proteome Coverage We built and characterised a mass spectrometer capable of performing CID (both beam type and resonant type), UVPD, EID and ECD in an automated fashion during an LCMS type experiment. We exploited this...

I am really pleased we managed to squeeze this story out during #ASMS2025. This is our contribution relating to the fantastic Omnitrap/Orbitrap. What we thought would be a straightforward conversation of our exploris-omnitrap turned into quite a journey. (1/n)

www.biorxiv.org/cgi/content/...

YouTube video by Amanpour and Company Breakthrough Prize-Winning Biochemist on the Deadly Cost of Funding Cuts | Amanpour and Company

David Liu @harvard.edu beautifully articulates the criticality of basic science funding for developing revolutionary therapeutics like life-saving base editors 👏

youtu.be/8YhJM6zxYDw?...

Patient-Specific In Vivo Gene Editing to Treat a Rare Genetic Disease | NEJM Base editors can correct disease-causing genetic variants. After a neonate had received a diagnosis of severe carbamoyl-phosphate synthetase 1 deficiency, a disease with an estimated 50% mortality ...

Amazing science, all within seven months of the patient's birth:
www.nejm.org/doi/full/10....

Which FDA-approved vaccines had randomized, placebo-controlled trials?

ALL OF THEM.

Polio?
Measles, mumps, rubella?
Haemophilus influenzae B?
Diphtheria, tetanus, pertussis?
Meningococcus?
Varicella?
Pneumococcus?
Rotavirus?
RSV?
Hepatitis B?
Influenza?
HPV?
COVID-19?
Shingles?

YEP.

A thread🧵
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