I am INCREDIBLY proud to share our lab’s first preprint, after 22 months of work!

A result of Dr. Anna Schreiber @annaschreiber.bsky.social and Dr. Anamika Gupta’s fantastic work, we focus on an ultra rare developmental disease, YWHAG syndrome.

(1/?)

www.biorxiv.org/content/10.6...

Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies A recent clinical study tested the effects of two different monoclonal antibodies (mAbs) (siltuximab, anti-IL6; tocilizumab, anti-IL6R) on the fate and function of T-cells in people with type 1 diabetes. While both mAbs affect the response of T-cells to stimulation, they have very different, sometimes opposing mechanisms. Here, we use mass-spectrometry based proteomics to analyze longitudinal serum samples (baseline and two weeks post-treatment) from 20 clinical trial participants to examine the effects of siltuximab and tocilizumab on extracellular vesicles. To accomplish this, serum samples were enriched for extracellular vesicles with Mag-Net and analyzed by LC-MS/MS to identify significantly differentially abundant protein groups and pathways. Proteome analysis confirmed highly reproducible measurements across multiple draw dates. In total, we quantified 3300 protein groups of which 46 protein groups had significantly altered abundance after mAb treatment. Tocilizumab altered pathways associated with proteostasis (neddylation) and pre-notch transcription and translation. Siltuximab altered FCGR activation pathway members. In addition, quantitation of the monoclonal antibody therapies themselves enabled the measurement of the correlation between drug amounts and impacted proteins. Taken together, this work demonstrates the utility of the Mag-Net method to evaluate the impacts of therapeutic interventions on serum extracellular vesicles.

(BioRxiv All) Serum proteomics reveals distinct phenotypic signatures to IL-6 blockade between two immunotherapies: A recent clinical study tested the effects of two different monoclonal antibodies (mAbs) (siltuximab, anti-IL6; tocilizumab, anti-IL6R) on the fate and function… #BioRxiv #MassSpecRSS

I love chromoproteins so much!

Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells link.springer.com/ar...

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#proteomics #prot-paper

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

With 𝗗𝗜𝗔-𝗡𝗡 𝟮.𝟯.𝟬 Preview (Academia-only for now), we showcase the transformative new capabilities that have been developed in the past months. Download: github.com/vdemichev/Di...

In vivo crosslinking and effective 2D enrichment for proteome wide interactome studies www.nature.com/artic...

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#proteomics #prot-paper

PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio...

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#proteomics #prot-paper

Native, Spatiotemporal Profiling of the Global Human Regulome The regulome, comprising transcription factors, cofactors, chromatin remodelers, and other regulatory proteins, forms the core machinery by which cells interpret signals and execute gene expression pr...

Here we go, my first skeet-torial(?) on Bluesky for my first paper from @talusbio.bsky.social !

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

This preprint describes our scalable, mass spec-based method for measuring which (and how many of them) proteins are interacting with DNA.

1/?

‼️ Job alert 🚨: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. 🧪🧪 So if you want to do cool stuff in protein MS, please apply ! ⬇️ Please RT
www.verwaltung.uni-halle.de/dezern3/Auss...

#Academicsky
#Chemsky
#teammassspec

Philadelphia.

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis p...

Error control in proteomics mass spectrometry analysis is hard. We came up with a way to evaluate error control. Upshot: for old-school DDA data, not so bad. For DIA data, no existing tool successfully controls the false discovery rate!

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

Favorite piece of vendor swag from ASMS.

Starting to work on something 👀

DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...

📢 Save the date!

The applications for the Empowerment Award for Q3 2025 will open soon 🏆

You can find more information here ➡️ femalesinms.com/empowerment/

New photo-crosslinker just dropped 👀

Heterobifunctional by warhead, K-K reactive, and partially tris tolerant.

I believe that this could be made into a cleavable version by reducing compound 1b to a primary amine and reacting with DSC to make an NHS-carbamate instead of an NHS-ester. Great work.

✈️ ASMS 2025 Early Career Researcher Travel Awards ✈️
📢 Call for Applications 📢
Don’t miss this opportunity!
Applications are open from *May 12th to 23rd* 📧
hispanicsandlatinxinms.org/asms-2025-ea...

#ASMS2025 #MSCommunity

Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!

Snapshot of in-cell protein contact sites reveals new host factors and hijacking of paraspeckles during influenza A virus infection Influenza A virus (IAV) exploits the host cellular machinery to facilitate its replication, yet many host-IAV interactions remain unexplored in the cellular context. Detailed information about interac...

This is a really nice application of XLMS to look at viral-host protein interaction. Impressive work from Fan Liu, giving me lots of ideas.

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

🧪 I was a postdoc at NIH 25 years ago. Without this experience I would not have been able to understand the beauty and power of science. I am now telling my students how important it is to stand up for science. 🧪 Otherwise ignorance will win.
@standupforscience.bsky.social
#supportscience
#saveNIH

City Hall, Philly.
Thinking of all of the NIH scientists right now.

Found out that BLAST is down while working on a project that I need it for. Absolutely bonkers that critical bioinformatics tools are being slashed.

LET'S GOOOO

A great first day

It begins!

Rooting around in ProteomeXchange today, and developing a deep desperation for people to name their rawfiles clearly.

Fried my old motherboard last week but have now upgraded enough to do proteomics at home 👀

DIA-NN 2.0 release is almost ready, will come with some big news. One is scanning methods support, at the moment doing some tuning of the algorithm using Synchro-PASEF data :) Turns out, 'Q1 information' is really helpful for gaining peptidoform confidence. Likely also channel-confidence in plexDIA.

Took a run to work on my day off (ran too many instances of DIA-NN and was justly punished with a crash) but was gifted an absolutely bonkers street find on the Philly curb. Greatest city in America, etc.