Founder of Aptila Biotech. Proteomics technologies and applications, DIA-NN author.
Berlin, Germany
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We are delighted to present DIA-NN 2.5. Redefining LC-MS proteomics with up to 70% more proteins identified and powerful capabilities for statistics, visualisation and biological interpretation.
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Vadim Demichev retweeted
New preprint: with ADAPT-MS, discovery plasma proteomics becomes a diagnostic tool for ovarian cancer. We separate benign from malignant adnexal masses and generalize to 5 validation cohorts. Collaboration with @ErnstLengyel @OvCa_UChicago.
medrxiv.org/content/10.64898…
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Means everyone can now get the full package for proteomics from Thermo: the MS + Evosep + DIA-NN!
Today, Evosep announced a new reseller agreement with Thermo Fisher Scientific, through which Thermo Fisher Scientific will offer the Evosep Eno separation platform as part of its mass spectrometry solutions portfolio.
Read the press release here: evosep.com/wp-content/upload…
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We have released DIA-NN 2.7. Performance improvements (more proteins) and GUI improvements. In particular, added a data completeness filter for pathway analysis. Further feedback on how to improve statistics and visualisation in DIA-NN is very welcome!
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Download links: github.com/vdemichev/DiaNN
Full release notes: github.com/vdemichev/DiaNN/d…
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Vadim Demichev retweeted
Proteomics analysis has always lived in its own universe. AlphaPeptTools puts it in #scverse instead, so that proteome, transcriptome & spatial data sit in one ecosystem. 11 search engines (DDA+DIA) read in, proteomics-specific statistics, #scverse native.
doi.org/10.64898/2026.09.11.…
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Vadim Demichev retweeted
Same single cell, two modalities—both at depth. We digest protein first, run Smart-seq3xpress + C18 (Evotip) separation: peptides captured, cDNA in flowthrough. In HeLa & stem cells, proteome tracks cell state; RNA variance flags transitioning cells.
biorxiv.org/content/10.64898…
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Vadim Demichev retweeted
New preprint: We used Deep Visual Proteomics to map vascular smooth muscle cell phenotypes in 24 human atherosclerotic plaques, cell-type & spatially resolved. Unstable plaques lose contractile and gain dedifferentiated states.
biorxiv.org/content/10.64898…
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Vadim Demichev retweeted
New preprint: Cell-type-resolved spatial proteogenomics, matched genome & proteome of the same cells. The trick: the flowthrough we normally discard after loading peptides onto an Evotip contains genomic DNA at 85–95% yield. One tip, two molecular layers.
biorxiv.org/content/10.64898…
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Vadim Demichev retweeted
Our proteomics study of carotid plaque vulnerability is out in @NatureCVR — with Ankit Sinha & Lars Maegdefessel @TU_Muenchen. Our unique methodologies and integrative analysis highlight molecular and spatial diversity present in plaque tissues. nature.com/articles/s44161-0…
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We have released DIA-NN 2.6! Multiple small improvements and a highlight: major advances in DDA data processing. Links in comments below.
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Release notes: github.com/vdemichev/DiaNN/d…
DDA benchmark: aptila.bio/blog/diann-26-dda…
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We preprinted a method of measuring phosphosite stoichimetries (occupancies) in just two mass spectrometry acquisitions, using internal stable isotope labelled controls.
In fact, we measure phospho stoichiometries in two ways, using dephosphorylation and using known relative ionisation efficiencies of phosphopeptides, compared to their unmodified forms: the measurements correlate well. In either case, estimates are well below on average compared to what was reported in some previous works. Link in comments below.
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Our machine learning driven quantification algorithm for proteomics now published in Nature Biotechnology. Optimal protein quantification and, for the first time, error estimates for individual quantities. Paper link in comments below.
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QuantUMS is the default method in our DIA-NN software.
nature.com/articles/s41587-0…
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Great to see DIA-NN 2.5 Enterprise already used in cutting edge publications.
TomAP-MS: an improved tomato lectin affinity purification-based mass spectrometry workflow enabling ultra-deep plasma proteomics: over 7500 proteins from plasma on Orbitrap Astral at 16 SPD and 6500 at 50 SPD.
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We have released DIA-NN 2.5.1 update with minor GUI changes.
We would be grateful for feedback and suggestions on the new statistics, visualisation and biological interpretation functionality introduced in DIA-NN 2.5. What can we make better? Any extras we can add?
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Full release notes: github.com/vdemichev/DiaNN/d….
Academia: github.com/vdemichev/DiaNN/r….
Enterprise: 2.5.1 available by the same link as all other 2.0+ versions.
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We are delighted to present DIA-NN 2.5. Redefining LC-MS proteomics with up to 70% more proteins identified and powerful capabilities for statistics, visualisation and biological interpretation.
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Release notes: github.com/vdemichev/DiaNN/d…
The new DIA-NN 2.5 is available for download from the same secure link (Enterprise customers) or GitHub (Academia version for non-profits).
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