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vadim-demichev.bsky.social
Group Leader at Charité – Universitätsmedizin Berlin. Proteomics technologies and applications, DIA-NN author. https://aptila.bio
68 posts 1,055 followers 1,041 following
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Preprint just out: Our international team's perspective on proteomics and AI, led by Tiannan Guo. We outline key areas where global collaboration between AI and proteomics researchers can accelerate biological discoveries and medical applications. Check it out: arxiv.org/abs/2502.15867

submitted 1 day ago • 1 comment

🚀 New preprint alert! We've improved IM2Deep for accurate peptide collisional cross-section (CCS) prediction, even for peptides exhibiting multiple conformations in the gas phase! 🎯 Check it out here: www.biorxiv.org/content/10.1...

submitted 3 days ago • 1 comment

Heck Yeah, I just searched over 300 timsTOF HT diaPASEF files with DIA-NN 2.0 on my cluster in under 2 hours. I'll try and make a video of how I did it tomorrow. It's not that terribly hard

submitted 6 days ago • 3 comments

Mass calibration algorithm in DIA-NN 2.0 can successfully correct even for the below 🙄😊. Apparently this kind of things can happen to some instruments. If you spot sth odd in your data - please always let us know, sometimes troubleshooting is really quick and interesting things are discovered.

submitted 7 days ago • 2 comments

pubs.acs.org/doi/10.1021/... Exciting to get this paper into press! It's a game changer to be able to search thousands of files from Astral on the order of hours.

submitted 12 days ago • 0 comments

The DIA-NN 2.0.2 update (now released) brings some speed improvements for very large runs (e.g. long-gradient Slice-PASEF) and also somewhat faster neural network training.

submitted 12 days ago • 0 comments

Popularity of current DIA data analysis tools (vendor-independent, based on citations of initial publication) Updated for 2024:

submitted 12 days ago • 1 comment

In this recently published viewpoint, we look at the promising technique of de novo sequencing and the application of computational algorithms/software to metaproteomics: doi.org/10.1002/pmic... #TeamMassSpec #Proteomics #Metaproteomics #Bioinformatics

submitted 23 days ago • 0 comments

I’ve been trying out the new DIA-NN package from @vadim-demichev.bsky.social for #proteomics. The new .parquet format is nice to work with. There’s a viewer for Windows: github.com/mukunku/Parq..., allows visual check and can save subsets to .csv or .xls.

submitted 26 days ago • 1 comment

DIA-NN 2.0 is released! We consider it the biggest step forward in the history of DIA-NN. On modern LC-MS almost all identifications are now peptidoform-confident, with major improvements e.g. for phospho. Some other cool things too: github.com/vdemichev/Di...

submitted 28 days ago • 7 comments

The EuPA proteomics awards committee invites you to apply for six 2024 EuPA awards that will be handed out personally at #EuPA2025 congress in Saint-Malo, France. 🥳 Deadline for applying is February 14! Here you can find the links to the application forms: eupa.org/2024-eupa-aw...

submitted 29 days ago • 0 comments

This is my inaugural BlueSky post! And I’m pleased that it is to announce the next LPDG meeting!Feb 20th with some really good speakers! To be held at Kings college with sponsorship from @davebrittain.bsky.social and special shout out to Steve Lynam for help with organising.

submitted 30 days ago • 0 comments

Cell Storage Conditions Impact Single-Cell Proteomic Landscapes #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

submitted 32 days ago • 0 comments

Weather’s going wild, and now your mass spec data’s a mess too? Coindidence? Nope! We reveal how weather-driven air pressure fluctuations impact diaPASEF-based high troughput proteomics - and how to fix it! Check out our new paper! #diaPASEF #Weatheromics pubs.acs.org/doi/10.1021/...

submitted 33 days ago • 5 comments

Did you already here about our travel grants for #EuPA2025? Don't miss this great opportunity to get a financial support to travel to Saint-Malo and join this years conference. Here you can find the link to the application: docs.google.com/forms/d/e/1F.... We are looking forward to your abstract! 🤩

submitted 33 days ago • 0 comments

We have #postdoc openings in proteomics and structural+computational+cell biology. We offer cutting-edge infrastructure and an interdisciplinary engaging environment. Check out our ongoing research and recent papers at www.theliulab.com Interested? Message me here or at www.theliulab.com/contact

submitted 37 days ago • 0 comments

Identification numbers and FDR control of Spectronaut 18 vs DIA-NN 1.9 as benchmarked by Jesper Olsen and colleagues (Nature Methods) www.nature.com/articles/s41...

submitted 41 days ago • 1 comment

We are excited to share our new Nature Methods paper describing the Chip-Tip workflow for single-cell proteomics identifying >5,000 proteins in single cells, enabling PTM analysis without enrichment and throughput of up to 120 single cell samples per day: rdcu.be/d6qJe

submitted 41 days ago • 0 comments

Our mipDVP workflow integrates 22-marker imaging with Deep Visual Proteomics to spatially map cell-type proteomes in hot/cold tumors, revealing distinct immune landscapes, macrophage barriers, T cell adaptations to hypoxia & tumor heterogeneity. Online in Molecular Cell. doi.org/10.1016/j.mo...

submitted 43 days ago • 0 comments

Robust collection and processing for label-free single voxel proteomics www.nature.com/artic... --- #proteomics #prot-paper

submitted 43 days ago • 0 comments

Hi, Just moved away from X and started here. Good moment to show a recent BlueSky picture I took in the Himalaya's. Hope Bluesky allows us to get back to more relevant posts.

submitted 46 days ago • 5 comments

It's the proteome, not just individual proteins. The levels of different proteins are linked to each other and the phenotype. This incredible work by Maik Pietzner, Claudia Langenberg and colleagues shows how to explore these connections based on large-scale plasma proteomics data.

submitted 44 days ago • 1 comment

Data is there to be reanalysed! Integrated View of Baseline Protein Expression in Human Tissues Using Public Data Independent Acquisition Data Sets pubs.acs.org/doi/full/10....

submitted 46 days ago • 1 comment

When Pharma validates the findings, they will use the best per $ method available. Guess which technology it’s gonna be? 😊 This project is awesome news for the field of proteomics newsroom.thermofisher.com/newsroom/pre...

submitted 47 days ago • 0 comments