Vadim Demichev

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.

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/10.648…

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/10.648…

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/s4416…

@lgamon In Experiment Design tab you can rearrange the runs based on metadata

@DemichevLab Also is it possible to force arrange by injection number? Any way you could make a QC to identify under/overloading? Peak width FWHM is helpful but we often see tims overloading and then you can see MS1:MS2 ratios fall apart, also MS1:precursorIDs etc

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?

@lgamon Another very useful one is IM vs m/z plot: can clearly see the boundaries of DIA windows on it, and can see if those don't properly cover the ion cloud

@lgamon Yes, DIA-NN reports interquartile range in trends.pdf auto-generated PDF report, also QC Dashboard.

@ardongre Now in 2.6: includes PG QuantUMS quality boxplots (interquartile) per run in QC Dashboard.

@DemichevLab How about QC metrics on bottom 1/4 or bottom 1/5 of PGs. If that is too many PGs then maybe bottom 200 PGs.

Release notes: github.com/vdemichev/DiaN… DDA benchmark: aptila.bio/blog/diann-26-…

We have released DIA-NN 2.6! Multiple small improvements and a highlight: major advances in DDA data processing. Links in comments below.

Yes, we increased contrast for checkbox labels in 2.5.1, after multiple requests, but the grey text over dropdowns stayed same. The reason is reducing visual clutter: if we make everything contrasty, it makes things harder to distinguish. This lead to a decision to make always-static captions pale, compared to actual settings, allowing one to better read the latter on a quick glance. Yes, it’s fully custom explorer. Reason: default Windows one may take seconds (!!!) to open on systems with network or cloud drives synced. This is a significant hurdle, so we needed a replacement. Suggestions on how to improve it are welcome!

@DemichevLab Has anyone else found the GUI hard to read? The gray text has low contrast on a white background. Dark mode is better, but some text, like “Spectral library,” is still hard to read. I found 2.3.2 more readable. Also, opening files no longer uses Windows’ default file explorer.

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.

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.

QuantUMS is the default method in our DIA-NN software. nature.com/articles/s4158…

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.

@kevinhou22 Great to see GCP project support, however Antigravity 2.0 does not pick up ADC, this pretty much precludes enterprise use. Also, I assume use behind proxy still not supported? We love the app, but these two features are essential (and supported by gemini-cli).

Antigravity IDE is just now a separate app from Antigravity 2.0! I spend most of my time in 2.0 personally and use it to review diffs + view files. I still hop into the IDE for some of my work...or if I'm feeling nostalgic for autocomplete / want to handwrite some artisan code line by line 🙂 The future of coding is agentic and we wanted to give users the option to use either or both the agent-first 2.0 experience or the traditional IDE experience. Same agent, same models, different form factors. More context: for existing AGY users, Antigravity IDE was merely renamed and is still installed on your machine. If you're a new 2.0 user and want the IDE, you download it from our website separately: antigravity.google/download

Preprint: biorxiv.org/content/10.648…

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.

Full release notes: github.com/vdemichev/DiaN…. Academia: github.com/vdemichev/DiaN…. Enterprise: 2.5.1 available by the same link as all other 2.0+ versions.

Release notes: github.com/vdemichev/DiaN… The new DIA-NN 2.5 is available for download from the same secure link (Enterprise customers) or GitHub (Academia version for non-profits).