Vadim Demichev

Most likely only one isoform will be reported, matching the better of the spectra

Very unlikely to get identified correctly

Yes, it will. Although without MS/MS evidence the reported localisation confidence will be low and the overall numbers of correctly assigned isomers are likely to be low. Those IDs with MS/MS evidence should be fine though.

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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, ...

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...

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...

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/...

Multiplexed Nanoparticle Protein Corona Enables Accurate and Precise Deep Plasma Proteomics The Proteograph Product Suite, a multiplexed nanoparticle (NP) protein corona-based workflow, substantially improves the depth of detection of proteins by mass spectrometry (MS) by compressing the dyn...

I'm excited to see this paper in press!

pubs.acs.org/doi/10.1021/...

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...

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...

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.

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...

I think this may change with MBR on samples from different patients, in particular for neat.

That said, it's definitely a good idea for us to provide a tutorial and example code on this. Will add to todo list.

Currently not saved automatically, main issue: a peptide can match multiple positions even within the sequence of a single protein. However, this can be done with a script, matching to protein sequence in protein_description.tsv output file. AI will easily write such a script in 5 min :)

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.

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!

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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.

Probably not, we are completely overwhelmed with paper writing at the moment, so only selected stuff eventually will get published. Short application notes are more likely though:)

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...

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...

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)

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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

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...

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...

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:

Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data Independent Acquisition Oxidative damage plays a critical role in various diseases including cardiovascular and neurological disorders. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure a...

Paper: pubs.acs.org/doi/full/10.... (for benchmark: see supplementary figure S2)

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):...

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-...

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...

Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics Quantitative mass spectrometry (MS)-based proteomics has become a streamlined technology with a wide range of usage. Many emerging applications, such as single-cell proteomics, spatial proteomics of t...

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

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:

Doctoral fellow

PhD Job Alert:
PhD position in metaproteome bioinformatics in Ghent/Belgium with a stay at RKI in Berlin.

www.ugent.be/en/work/scie...

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On my way to ESCP. Super looking forward to this awesome meeting!

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