Vadim Demichev
@vadim-demichev.bsky.social
Group Leader at Charité – Universitätsmedizin Berlin. Proteomics technologies and applications, DIA-NN author. https://aptila.bio
Pinned
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...
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...
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
November 19, 2025 at 10:07 AM
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...
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
Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications
Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...
www.nature.com
November 6, 2025 at 3:49 PM
Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Vadim Demichev
Happy 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 ⬇️
November 5, 2025 at 10:15 AM
Happy 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 ⬇️
Reposted by Vadim Demichev
GO FAST with InfinDIA!! proteomicsnews.blogspot.com/2025/10/tire...
Tired of slow DIA search times? Try DIA-NN 2.3 with InfinDIA!
Is your awesome new instrument generating so much data that you can't process it fast anymore? My data density has jumped about 5x from my...
proteomicsnews.blogspot.com
October 2, 2025 at 11:01 AM
GO FAST with InfinDIA!! proteomicsnews.blogspot.com/2025/10/tire...
Reposted by Vadim Demichev
We are #hiring! 🚀
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Software Developer
You will contribute to the development of core database applications, web services, data ingestion workflows, and the PRIDE Web platform as part of the PRIDE ecosystem. Working closely with the team, ...
embl.wd103.myworkdayjobs.com
October 23, 2025 at 1:38 PM
We are #hiring! 🚀
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
#PRIDE team is looking for a developer to build its future infrastructure. Our focus in a nutshell: #bigdata, single cell proteomics #SCP, & an #AI-oriented platform. Join us to shape the future of open proteomics data!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Reposted by Vadim Demichev
Excited to see this published in JPR. For years I've wanted a simple way to standardize the signal between instruments. We use the precision of an intraspectrum ratio to assess the relationship between the reported signal and the number of ions. pubs.acs.org/doi/10.1021/...
Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists
Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...
pubs.acs.org
October 22, 2025 at 3:32 PM
Excited to see this published in JPR. For years I've wanted a simple way to standardize the signal between instruments. We use the precision of an intraspectrum ratio to assess the relationship between the reported signal and the number of ions. pubs.acs.org/doi/10.1021/...
Reposted by Vadim Demichev
Reposted by Vadim Demichev
new 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...
The functional landscape of the human ubiquitinome
Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...
www.biorxiv.org
October 9, 2025 at 7:07 AM
new 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...
www.linkedin.com/pulse/pre-tr...
Pre-trained DIA models can 'covertly' inflate FDR - and this will not show up in entrapment validation
Transformer models are great? For several years, there has been this idea that one can pre-train advanced deep learning models, e.g.
www.linkedin.com
October 9, 2025 at 11:41 AM
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...
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.
October 7, 2025 at 12:33 PM
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
Do you have an exciting experiment that you'd love to do using proteomics in the context of your work? YPIC funds 5000 eur for your research idea to come to life!
⬇️⬇️⬇️⬇️⬇️
⬇️⬇️⬇️⬇️⬇️
🎉 Exciting opportunity for students in proteomics! 🎉
The Student Proteomics Fund (SPF) is back!
📅 Key dates:
Call opens: October 1, 2025
Submission deadline: November 30, 2025
Don’t miss your chance to bring your research idea to life!
New boost
#SPF #YPIC #Proteomics
The Student Proteomics Fund (SPF) is back!
📅 Key dates:
Call opens: October 1, 2025
Submission deadline: November 30, 2025
Don’t miss your chance to bring your research idea to life!
New boost
#SPF #YPIC #Proteomics
October 6, 2025 at 6:08 AM
Do you have an exciting experiment that you'd love to do using proteomics in the context of your work? YPIC funds 5000 eur for your research idea to come to life!
⬇️⬇️⬇️⬇️⬇️
⬇️⬇️⬇️⬇️⬇️
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...
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
October 1, 2025 at 7:19 AM
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.
September 29, 2025 at 11:46 AM
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...
September 26, 2025 at 9:52 AM
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
Are you using DIA mass spectrometry in proteomics?
We have just put this paper online: www.biorxiv.org/content/10.1...
Here, we came up with some Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)
1/4
We have just put this paper online: www.biorxiv.org/content/10.1...
Here, we came up with some Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)
1/4
Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)
Advances in mass spectrometry and associated computational tools have resulted in the wide-spread adoption of Data-Independent Acquisition (DIA) for proteomics. Experiments using state-of-the-art inst...
eur03.safelinks.protection.outlook.com
September 23, 2025 at 9:44 AM
Are you using DIA mass spectrometry in proteomics?
We have just put this paper online: www.biorxiv.org/content/10.1...
Here, we came up with some Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)
1/4
We have just put this paper online: www.biorxiv.org/content/10.1...
Here, we came up with some Recommendations for Quantitative Data-Independent Acquisition (DIA) Proteomics using Controlled Quantitative Experiments (CQEs)
1/4
Reposted by Vadim Demichev
Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Start Page: /home/software/Skyline/events/2025 Webinars/Webinar 26
skyline.ms
September 15, 2025 at 8:26 AM
Proteomics Webinar: DIA with FragPipe, DIA-NN, and Skyline
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Presenters: Eduard Sabidó and Brendan MacLean
When: Tuesday, September 16, 8am (Pacific Time)
Register Now ... skyline.ms/project/home...
#massspec #proteomics
Reposted by Vadim Demichev
New 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...
- 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...
Release v0.0.34 - DIANN and MaxDIA support · bigbio/pmultiqc
What's Changed
fix bugs and add plots for mzid by @yueqixuan in #295
Multiple fix in mzidentml by @ypriverol in #296
MaxQuant: Fix NaN intensity errors by @cbielow in #304
Fix bug in proteobench_u...
github.com
September 12, 2025 at 12:47 PM
New 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...
- 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
Out in @cp-cellsystems.bsky.social: Deep Visual Proteomics shows xenotransplantation drives colon #organoids toward in-vivo-like proteomes supporting their use in regenerative medicine; culture tweaks can mimic this shift. With @kimbakjensen.bsky.social. Lead author Frederik Post explains below:
September 10, 2025 at 3:16 PM
Out in @cp-cellsystems.bsky.social: Deep Visual Proteomics shows xenotransplantation drives colon #organoids toward in-vivo-like proteomes supporting their use in regenerative medicine; culture tweaks can mimic this shift. With @kimbakjensen.bsky.social. Lead author Frederik Post explains below:
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-...
www.linkedin.com/posts/vadim-...
𝐖𝐡𝐲 𝐃𝐈𝐀-𝐍𝐍 𝐢𝐬 𝐠𝐫𝐞𝐚𝐭 𝐟𝐨𝐫 𝐜𝐡𝐞𝐦𝐨𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬?
You can analyse almost anything with it, and with high data quality:
Below is an excellent benchmark by Ana Martínez del Val… | Vadim Demichev
𝐖𝐡𝐲 𝐃𝐈𝐀-𝐍𝐍 𝐢𝐬 𝐠𝐫𝐞𝐚𝐭 𝐟𝐨𝐫 𝐜𝐡𝐞𝐦𝐨𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬?
You can analyse almost anything with it, and with high data quality:
Below is an excellent benchmark by Ana Martínez del Val and colleagues. Bottom panel (c):...
www.linkedin.com
September 9, 2025 at 7:15 AM
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-...
www.linkedin.com/posts/vadim-...
Reposted by Vadim Demichev
Major 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...
- 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...
Release v2.10.4 · PRIDE-Archive/px-submission-tool
🚀 PX Submission Tool v2.10.4
📦 Downloads
Versioned: px-submission-tool-v2.10.4.zip
Latest: px-submission-tool-latest.zip (always points to current version)
🔗 Universal Links
Latest Release: http...
github.com
September 5, 2025 at 9:10 AM
Major 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...
- 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:
September 2, 2025 at 5:58 PM
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 Demichev
PhD 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
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
Doctoral fellow
www.ugent.be
August 26, 2025 at 9:04 PM
PhD 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
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/
Hotel rooms in Vienna are inexpensive.
www.apma.at/6thescp/
6th ESCP 2025 – APMA
www.apma.at
August 25, 2025 at 12:59 PM
On my way to ESCP. Super looking forward to this awesome meeting!
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
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
July 11, 2025 at 8:43 AM
🚀 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
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
Reposted by Vadim Demichev
New preprint reveals why IDO1 inhibitor trials failed! Led by Peter Murray @mpibiochem.bsky.social our collaboration discovered IDO1 actually kills ovarian cancer cells via GCN2/ISR pathway - not protecting them. Spatial proteomics uncovers unexpected biology.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Spatial proteomics reveals mechanisms of cell-intrinsic tryptophan metabolism controlling ovarian cancer survival
Indole-2,3-dioxygenase (IDO1) depletes tryptophan to dampen anti‑tumor T cells, yet IDO1 inhibitors (IDO1i) have failed clinically. Using deep visual proteomics, we isolated IDO1 high, medium and low ...
www.biorxiv.org
August 20, 2025 at 5:15 AM
New preprint reveals why IDO1 inhibitor trials failed! Led by Peter Murray @mpibiochem.bsky.social our collaboration discovered IDO1 actually kills ovarian cancer cells via GCN2/ISR pathway - not protecting them. Spatial proteomics uncovers unexpected biology.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...