Bar charts comparing the quantification of peptide groups in DDA and DIA data across different datasets and conditions.

🔄 Fig 6: CHIMERYS enables fair DDA vs DIA comparisons.
→ Same algorithm, consistent FDR
→ IDs vs data completeness: tune your workflow to your needs
Unify your data analysis workflow with #CHIMERYS: choose the mode, not the model!
7/7

A graph showing CHIMERYS deconvoluting chimeric spectra, with a comparison of measured versus precursor intensities. It highlights predicted and observed peaks for multiple peptides.

I'm truly excited to share the new Nature Methods publication of @msaid 🎉

We compare #CHIMERYS against state-of-the-art search engines for DDA/PRM/DIA, and even push into the realm of direct infusion #proteomics 🧪🔬

Huge thanks to the other co-first authors […]

[Original post on fediscience.org]

I'm truly excited to share MSAID's new publication in @naturemethods.bsky.social 🎉

We compare #CHIMERYS against state-of-the-art search engines for DDA/PRM/DIA, and even push into the realm of direct infusion #proteomics. Huge thanks to the other co-first authors and everyone involved #TeamMassSpec

Unifying the analysis of bottom-up proteomics data with CHIMERYS - Nature Methods CHIMERYS is a spectrum-centric and data acquisition method-agnostic algorithm for the analysis of MS2 spectra. It is capable of deconvoluting any MS2 spectrum, regardless of whether it was acquired by...

One algorithm to rule them all? CHIMERYS bridges the gap — DDA,DIA and PRM — together at last!
With #CHIMERYS, we can now directly compare DDA and DIA data — 🍎 to 🍎 finally made possible.
doi.org/10.1038/s41592-025-02663-w
#KusterLab #WilhelmLab #MSAID #Proteomics

So glad to see our paper describing #CHIMERYS finally published in @naturemethods.bsky.social ! Check it out!

🔄 Fig 6: CHIMERYS enables fair DDA vs DIA comparisons.
→ Same algorithm, consistent FDR
→ IDs vs data completeness: tune your workflow to your needs
Unify your data analysis workflow with #CHIMERYS: choose the mode, not the model!
7/7

🚨 New in @naturemethods.bsky.social
#CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow.
Wanna know how CHIMERYS works? 👉 www.nature.com/articles/s41...
#TeamMassSpec #NatureMethods #ASMS2025 🧪🔬
1/7

🔄 Fig 6: CHIMERYS enables fair DDA vs DIA comparisons.
→ Same algorithm, consistent FDR
→ IDs vs data completeness: tune your workflow to your needs
Unify your data analysis workflow with #CHIMERYS: choose the mode, not the model!

MSAID Platform

You could also try filtering your results at peptidoform q-value, which seems to be more stringent than the regular q-value. Otherwise, feel free to process the data with #CHIMERYS 4 at platform.msaid.io, where you can filter multiple rollup levels at run-specific and dataset-global q-value or PEP.