Both options are usable. For SN only directDIA is available, while TIMS DIANN uses a library-based approach

🔓No Library, no limits: accelerate immunopeptide discovery with #directDIA in Spectronaut® 20

✅ Up to 80% more HLA-I and 30% more HLA-II identifications
✅ Up to 80% faster analysis

👉 Read our blog to explore the data: biognosys.com/how-can-libr...

#Immunopeptidomics

🔥 #Immunopeptidomics analysis just leveled up with #Spectronaut20! directDIA delivers deeper, more confident insights than ever. Plus SpectroMine 5 now brings Kuiper to DDA, harmonizing your workflows.

Ready to upgrade? biognosys.com/software/spe...

#Spectronaut #DIAproteomics

35 variable window DIA.. 45 min active gradient.. Spectronaut directDIA analysis.. sample prep by DDM method.. but not quite a one pot method..

Process large data faster with #Spectronaut #directDIA parallelization in #AWS cloud. Learn how AWS Step Functions, Batch, FSx for Lustre, and S3 reduce computation time by up to 84% with robust, FDR-controlled results.⏱️

Download our poster: biognosys.com/resources/cl...

Our latest paper is out! 🧬 Discover how DIA-based immunopeptidomics reveals low-abundant Listeria epitopes. Next to Spectronaut directDIA and FragPipe diaTracer, we showcase the feasibility of using DIA-NN proteome-wide predicted immunopeptide libraries!

Read it here 👉 pubs.acs.org/doi/10.1021/...

This year, we are coming to #USHUPO2025 with 3 scientific posters!📊🧑‍🚀

Meet us to learn about library-free #DIA analysis, cloud-based parallelization for #directDIA method and advancing #plasma #biomarker discovery with our P2 Enrichment workflow!

Learn more👉 biognosys.com/conferences/...

You're invited!🚨Join the #Spectronaut 20 launch seminar and be the first to hear about our new search engine— and how it's changing the game for directDIA™.

📅June 3 @ 7:00 AM | Room 343-344

👉Register now before it's full! go.biognosys.com/l/984251/202...

#TeamMassSpec #ASMS2025

In Part 2 of our #Spectronaut 20 series, Daniel Green from Greywolf Therapeutics demonstrates how new advances in Spectronaut expand the ERAP1 inhibitor antigen landscape—delivering 47% more peptide discoveries with #directDIA.

Watch the seminar recording: biognosys.com/resources/in...

I think the biognosys folks would still do a little pierce HpH of a pooled sample DDA, then use that library plus directDIA (like what @lgamon.bsky.social just said). BUT, also I think the library free approaches are pretty great these days with the modeling.

🚀Kuiper in #Spectronaut ®20 delivers >70% more unspecific peptide IDs (including HLA I & II) in a fraction of the time, no library needed!

⚡Ditch outdated workflows: see our poster to break free from slow, library‑based searches👇 biognosys.com/resources/in...

#DIA #directDIA #MassSpectrometry

Get ready for a breakthrough in #directDIA with Spectronaut 20 and its new Kuiper search engine!

Kuiper redefines what's possible in #DIA by dramatically increasing speed and depth — even in the most complex search spaces!

Explore all new features: biognosys.com/software/spe...

One important part I forgot to mention, but Kuiper is completely data driven (purely an algorithmic solution) that is not dependent on any pre-trained HLA predictors. You don't need any prior knowledge of your samples to do a library-free, directDIA search using SN20 and Kuiper.

The runtime improvements are what is most impressive in my eyes. We can now do unspecific class-1 and class-2 in ~10 minutes per DIA raw file (library free, directDIA including all steps). That marks a 78% and 86% reduction in search time compared to SN19.

With Spectronaut I only did directDIA, for some reasons searching with a library was causing consistent blue screens of death on windows 11.

And with DIA-NN I didn't try searching all the files for the library as it would be much longer for less benefit.

oh, and forgot to mention. That was directDIA (but Kuiper can also be used to search DDA data as well)

Astral files, I searched ~375 raw files in about 1 day (server isn't amazing). 70 raw files from Timmy took like 2.5 days. This is all directDIA though I suppose I did use a smaller fasta for the astral search, so maybe not an entirely fair comparison 🤔