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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It is remarkable how we are able to improve the performance and capabilities of our DIA-NN proteomics software at an ever-increasing pace. Sneak peek at the upcoming DIA-NN 2.8 Enterprise:
- A major increase in identification numbers, in particular with InfinDIA: 25%+ on some datasets compared to 2.7.
- Support for three additional technologies beyond ordinary DIA and DDA. Guess which ones?
Back in the days of DIA-NN 1.8.1, released in early 2022, I genuinely thought we were close to the ceiling of how deeply we could see into the data. Turns out, that could not have been further from the truth.
We have achieved massive gains in proteomic depth over the past year, and the pace is accelerating. Each advance is a step not only towards properly utilising the full potential of the very expensive mass spectrometry instrumentation, but also towards our ability to extract more knowledge from existing data. Automated reanalysis of ProteomeXchange repositories at scale - who knows what we might find there?
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Vadim Demichev retweeted
Can MS-based proteomics see what histology can’t? We profiled 83 rare paediatric adrenocortical tumours from archival FFPE tissue & found 4 proteome-defined states that predict survival better. Now in @eBioMedicine, led by Rainer Claus & Andreas Metousis. doi.org/10.1016/j.ebiom.2026…
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Vadim Demichev retweeted
SPARCS: Deep Visual Proteomics-style laser microdissection meets genome-wide CRISPR screening. Find genes behind how cells look, isolate them, profile them by mass spec.
Now in @CellCellPress! Tweetorial from @niklas_a_s follows🧵
doi.org/10.1016/j.cell.2026.…
Out now in @CellCellPress: ✨SPARCS✨, a
platform for discovering the genes behind complex cellular phenotypes.
SPARCS combines Al-powered image analysis with automated laser microdissection to precisely isolate cells from large mutant libraries.
Paper and highlights👇(1/9)
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Aptila Biotech today announces a collaboration with IonOpticks, a global leader in high-performance chromatography solutions. Through this partnership, Aptila will support IonOpticks in deploying DIA-NN Enterprise across its chromatography systems and mass spectrometry method development, while IonOpticks will supply Aptila with state-of-the-art mass spectrometry data to help further optimise DIA-NN.
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Read the full press release aptila.bio/blog/aptila-ionop…
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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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