Devin Schweppe

During these uncertain times, I’m very happy to see that my institution, @scripps.edu has an open tenure-track Assistant Professor position. Any field in Chemistry or Biology is welcome. I’d especially love to see fellow neuroscientists apply. Please repost!

apply.interfolio.com/174756

AlphaDIA enables DIA transfer learning for feature-free proteomics - Nature Biotechnology An open-source platform for data-independent acquisition proteomics adapts predicted libraries to experimental settings.

AlphaDIA enables DIA transfer learning for feature-free proteomics - @mannlab.bsky.social @jalew188.bsky.social go.nature.com/4qmEQMM

Karel Svoboda and Jay Shendure elected to National Academy of Medicine The honor recognizes leaders who have demonstrated outstanding achievement and made lasting contributions to the advancement of the medical sciences, health care, and public health

Congratulations to Karel Svoboda and @jshendure.bsky.social on their election to the National Academy of Medicine (@nam.edu)! Election to the Academy is one of the highest honors in health and medicine. #NAMmtg

More on their journeys to this achievement: alleninstitute.org/news/karel-s...

Our group has a PhD position open in this Doctoral network. Our topic is around combining proteomics AI and protein structures. Look through the website below to look at all of the projects/groups and apply.

DNASE1L3 surveils mitochondrial DNA on the surface of distinct mammalian cells The extracellular space is a critical environment for discriminating self versus non-self nucleic acids and initiating the appropriate immune responses through signaling cascades to relay information ...

We’re excited to report work led by postdoc Jennifer Porat in the lab, finding that DNA accumulates on the surface of living cells and that the secreted extracellular protein DNASE1L3 can modulate its levels on B and T cells. With a new twist for ATAC-seq as well www.biorxiv.org/content/10.1...

My lab @stanfordmedicine.bsky.social is recruiting! We are looking for a postdoc at the interface of quantitative proteomics and G protein-coupled receptor (GPCR) biology:
postdocs.stanford.edu/prospective/...
#TeamMassSpec #Proteomics #GPCR #Postdoc

EEE meeting is BACK! Early Embryogenesis & Epigenetics conference in Berlin 02/2026.
Checkout great program and over 12 slots for (not so) short talks for submitted abstracts!. Early registration now open -
w.molgen.mpg.de/embryo2026

🚨 Our 4th example of metalloallosteric regulation of kinase activity. Out today in @CellReports with @KJSsci. The ER stress sensor kinase PERK needs copper to work. Without copper, PERK can’t protect cells under stress. cell.com/cell-reports/p…

New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...

I’ve seen the concept, but haven't seen a hive in action, fun to think about api control for linked MSs though!

Dosa: A method to covalently barcode proteins for high throughput biochemistry Deep mutational scanning couples a proteins activity to DNA sequencing for high throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like g...

#microsky

www.biorxiv.org/content/10.1...

Dosa: A method to covalently barcode proteins for high throughput biochemistry Deep mutational scanning couples a proteins activity to DNA sequencing for high throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like g...

www.biorxiv.org/content/10.1...

Thanks! Though we may have hit a ceiling with that one 😬

Real-Time Instrument Control across Multiple Orbitrap Platforms through a Single Software Interface Applications using real-time spectral analysis and real-time instrument control have emerged in recent years as powerful tools to improve the capabilities and sensitivity of mass spectrometers. Softwa...

Helios now out @ JPR: pubs.acs.org/doi/10.1021/...

NSF Graduate Research Fellowship Program (GRFP)

The GRFP lives!! (due end of October)
www.nsf.gov/funding/oppo...

Nova! Build all the mass spec tools! Playing catchup on posts this morning, I guess! This one looks super useful!  Don't wanna read? I gotcha.  https://schweppelab.github.io/N...

Thanks to @proteomicsnews.bsky.social for the shoutout on Nova as well!

proteomicsnews.blogspot.com/2025/07/nova...

Real-time API control of mass specs has been hard to get started (C#, VS, etc). Mike Hoopmann's recent work makes dev easier & more open!:

Nova - lightweight dev library
schweppelab.github.io/Nova/ pubs.acs.org/doi/full/10....

Helios - a unified instrument API now @ JPR
github.com/SchweppeLab/...

After five great years, my journey in the Schweppe Lab and at UW has come to a close. Huge thanks to @dschweppe.bsky.social and all the amazing labmates for making graduate school such a wonderful experience. Extremely grateful for the memories and all the help I received along the way.

Pediatric Brain Cancer Group to Lose Federal Funding

Let this one sink in.
www.nytimes.com/2025/08/28/w...

I am delighted to announce that the UW Department of Biochemistry has opened searches for TWO tenure-track positions.

Descriptions and links in the following two posts.

Spread the word - we at @stanford-chemh.bsky.social are searching to fill a new junior faculty at the interface of molecular and computational science. See link below!

Mapping early human blood cell differentiation using single-cell proteomics and transcriptomics Single-cell transcriptomics (scRNA-seq) has facilitated the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, the exclusive use of mRNA measurem...

We’re excited to present this integrative analysis of single-cell proteomics and transcriptomics of the human HSPC hierarchy. Now published in @science.org together with @fabiantheis.bsky.social, @erwinschoof.bsky.social, @porsebo.bsky.social.
www.science.org/doi/10.1126/...
🧵

Assistant Professor - Molecular, Cellular, and Developmental Neuroscience - Department of Neuroscience University of California, Berkeley is hiring. Apply now!

Come join our new Department of Neuroscience @ucberkeleyofficial.bsky.social as an Assistant Professor! aprecruit.berkeley.edu/JPF05041

Department members sit at a very long table in the hallway eating a pre-Thanksgiving potluck feast.

Faculty search announcement 2025: Tenure-Track Assistant Professor in Microbiology at UT Southwestern. We seek candidates working in microbial pathogenesis (some preference may be given to bacterial pathogens). Come join our community! (1/5) www.utsouthwestern.edu/departments/...

happy to say my new department is hiring an associate/full professor: academicjobsonline.org/ajo/jobs/30328

please apply!

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

The authors report that all seven tested deep learning models failed to outperform simple baselines in predicting transcriptome changes after single or double perturbations.

I will duck for cover.

About 800 NIH, NSF research grants suspended following UCLA federal funding cuts - Daily Bruin About 800 research grants have been suspended at UCLA, according to a Friday email from Vice Chancellor for Research and Creative Activities Roger Wakimoto. Wakimoto said in the email, which was sent ...

Daily Bruin article about the ~800 frozen grants at UCLA including some from my lab dailybruin.com/2025/08/02/a...

Post-Translational Modifications Remodel Proteome-Wide Ligandability Post-translational modifications (PTMs) vastly expand the diversity of human proteome, dynamically reshaping protein activity, interactions, and localization in response to environmental, pharmacologi...

Excited to share a new preprint from the lab. We show that PTMs like phosphorylation & glycosylation dynamically reshape proteome-wide ligandability in cells, including proteins like KRAS. Great collaboration with the Huang Lab, @forlilab.bsky.social and BMS. 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.

pubs.acs.org/doi/10.1021/...