Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells link.springer.com/ar...
---
#proteomics #prot-paper
๐งช
www.nature.com/articles/s41...
With ๐๐๐-๐ก๐ก ๐ฎ.๐ฏ.๐ฌ 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...
---
#proteomics #prot-paper
PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio...
---
#proteomics #prot-paper
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/?
โผ๏ธ Job alert ๐จ: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. ๐งช๐งช So if you want to do cool stuff in protein MS, please apply ! โฌ๏ธ Please RT
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
Philadelphia.
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 ๐
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...
๐ข Save the date!
The applications for the Empowerment Award for Q3 2025 will open soon ๐
You can find more information here โก๏ธ femalesinms.com/empowerment/
New photo-crosslinker just dropped ๐
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.
โ๏ธ ASMS 2025 Early Career Researcher Travel Awards โ๏ธ
๐ข Call for Applications ๐ข
Donโt miss this opportunity!
Applications are open from *May 12th to 23rd* ๐ง
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!
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...
๐งช 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. ๐งช 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 ๐
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.
Trying to get back into altering this year!
Being "friends" with students might actually be the underlying problem. Have you considered their perspective on the "friendship"? How can there be any friendship with such a strong power imbalance? Would they dare say no to the friendship if you are the one grading and paying them?
Received a couple of xlms projects in the core, and I literally could not be happier.
