Vadim Demichev
Group Leader at Charité – Universitätsmedizin Berlin. Proteomics technologies and applications, DIA-NN author. https://aptila.bio
- Reposted by Vadim DemichevSDRF 1.1 is almost here 🎉 Big format & tooling updates ahead. Thanks to the community! We’ll keep refining together. One key question just opened: should we remove prefixes for samples, data files & factor values? Join the discussion 👉 github.com/bigbio/prote... or let me know here.
- Reposted by Vadim DemichevA special opportunity for lovers of mass spectrometry proteomics to join a like-minded team at PTI. Join a collaborative initiative to enable direct protein analysis at unprecedented scale, in partnership with leading instrument developers, academics, and industry leaders. 1/2
- Reposted by Vadim DemichevI have a 3-year postdoc position available at University of Manchester for a mass spec expert in proteomics. The person will be involved in exciting projects in single cell proteomics, drug discovery and innate immunity - on timsTOF Ultra AIP & HF & Astral Zoom. www.jobs.ac.uk/job/DQJ093/r...
- Reposted by Vadim DemichevIt is my great honor to announce that registration for the 7th ESCP Single Cell Proteomics Conference is now open: lnkd.in/e4iyiQjf With around 250 participants, it is one of the largest SCP conferences worldwide. We are also proud to announce that there is no participation fee for our conference.
- Reposted by Vadim DemichevWant to make your DIA-NN QC reports in a web browser and then go back in time to the 80's and 90's? Now you can with my completely AI vibe coded streamline app! dia-nn-qc.streamlit.app You're welcome 😜
- Reposted by Vadim DemichevHow do you deal with missing values and "unique" proteins that were only identified in one condition in proteomics data? Mengchun Li, an amazing PhD student in my lab, developed this great Bayesian approach. Please try it and give feedback! www.biorxiv.org/content/10.6...
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- We acquired a large-scale mixed-species benchmark, with variable background, to comprehensively assess quantitative accuracy of proteomics. Our insights based on the data: www.biorxiv.org/content/10.6... PRIDE repo will be made public in the next days.
- We are delighted to release 𝐃𝐈𝐀-𝐍𝐍 𝟐.𝟑.𝟏, with a groundbreaking 𝐈𝐧𝐟𝐢𝐧𝐃𝐈𝐀 module for fast searches against huge databases and support for 𝐃𝐃𝐀 data. Release notes: github.com/vdemichev/Di...
- Reposted by Vadim Demichev[Not loaded yet]
- Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: dephosphorylation on-tip identifies the sequences of phosphorylated peptides. This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim DemichevHappy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️
- Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim DemichevI'm excited to see this paper in press! pubs.acs.org/doi/10.1021/...
- Reposted by Vadim Demichevnew preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...
- Wrote a short perspective: Pre-trained DIA models can 'covertly' inflate FDR - and this will not show up in entrapment validation www.linkedin.com/pulse/pre-tr...
- Precisely mapping proteases specificity and predicting cleavage rates - with peptide libraries: doi.org/10.1101/2025.... This is a powerful application that is uniquely enabled by the peptidoform confidence and QuantUMS modules in DIA-NN 2.0.
- Reposted by Vadim Demichev[Not loaded yet]
- I will be at the 𝐃𝐈𝐀-𝐍𝐍 session @ 𝐓𝐡𝐞𝐫𝐦𝐨 𝐏𝐫𝐨𝐭𝐞𝐨𝐦𝐞 𝐃𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐞𝐫 & 𝐂𝐨𝐦𝐩𝐨𝐮𝐧𝐝 𝐃𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐞𝐫 User Meetings in Bremen, Germany, 𝟗-𝟏𝟏 𝐃𝐞𝐜𝐞𝐦𝐛𝐞𝐫. With some cool advances for DIA-NN on Thermo instruments. www.thermofisher.com/de/de/home/e...
- In DIA-NN 2.3.0, we have added Deamidation (NQ) as an option in the GUI. There are good reasons for it :) You can try InfinDIA with any number of modifications selected, and check the RT differences between modified vs respective stripped peptides, for each mod - a way to validate peptidoform FDR.
- 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...
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim DemichevNew release of pmultiqc v0.0.34 🚀🎉. github.com/bigbio/pmult..., highlights: - A new contributor, Chris Bielow - MaxDIA support, thanks @maxquant.bsky.social pmultiqc.quantms.org/MaxDIA/multi... - DIANN reports way deeper thanks @vadim-demichev.bsky.social pmultiqc.quantms.org/DIANN/multiq...
- Reposted by Vadim Demichev[Not loaded yet]
- Chemoproteomics: can we trust the search engine? Since inception of DIA-NN, we always prioritised data quality. A nice benchmark by @anamdv.bsky.social and colleagues: www.linkedin.com/posts/vadim-...
- Reposted by Vadim DemichevMajor release of @pride-ebi.bsky.social submission tool: - Smarter Java setup — bundled JRE - Reliable file transfer logging with Aspera, FTP. - Clearer instructions and troubleshooting in the README - Automated releases through GitHub Actions, so updates are consistent github.com/PRIDE-Archiv...
- We have updated our Slice-PASEF preprint! It's a result of a large collaboration where we highlight its advantages for single cell proteomics. Or any other applications benefiting from sensitivity. For example, major gains for ubiquitinomics:
- Reposted by Vadim DemichevPhD Job Alert: PhD position in metaproteome bioinformatics in Ghent/Belgium with a stay at RKI in Berlin. www.ugent.be/en/work/scie... Feel free to share
- On my way to ESCP. Super looking forward to this awesome meeting!
- The European Symposium on Single Cell Proteomics (ESCP) will be held in Vienna for the 6th time, from August 26th – 27th 2025 This year's focus will include spatial proteomics studies on the single-cell level. There is no registration fee Hotel rooms in Vienna are inexpensive. www.apma.at/6thescp/
- Reposted by Vadim Demichev🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here! 💡 Create stunning, shareable HTML reports for your collaborators in seconds. ✨ Try pmultiqc.quantms.org Examples👇 #Proteomics #QC
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim DemichevLocalisation of Organelle Proteins using Data-Independent Acquisition (DIA-LOP) www.sciencedirect.co... --- #proteomics #prot-paper
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Was a great pleasure to contribute to this work pubs.acs.org/doi/10.1021/.... DIA-NN release with support soon.
- Time and time again, it's always the same picture. DIA-NN controls FDR correctly as data reliability has been the main goal at DIA-NN's conception back in 2017 and a priority since then.
- Reposted by Vadim DemichevUnexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".
- Assessing FDR in proteomics using full proteome recombinant libraries: pubs.acs.org/doi/full/10..... A very elegant work and a benchmarking dataset useful for many other things too. Protein FDR higher than precursor FDR likely due to paralogues - and this needs to be researched further.
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim DemichevWe are looking for a student representative for BSPR. Its an exciting opportunity to be more involved with the society anf help shape its future. Please do consider joining #bspr2025
- Reposted by Vadim Demichev[Not loaded yet]
- (1/2) We have always validated FDR internally on several datasets. Bo Wen and colleagues discovered that FDR of DIA-NN 1.8.1 was anti-conservative on some (but not other) datasets - for some unknown reason. So we fixed it in 2.0 :) Now q-values are more accurate and fluctate less across datasets.
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim Demichev[Not loaded yet]
- Reposted by Vadim DemichevPumped to finally show off our spatial proteomics work presented a few weeks ago at the EAS Congress @eassociety.bsky.social and now live on @biorxivpreprint.bsky.social 🥳 Time for a science thread! #TeamMassSpec #SpatialProteomics #AtheroSky 🧵 www.biorxiv.org/content/10.1...
