🚨 New in @naturemethods #CHIMERYS has already transformed #proteomics since 2022, powering DDA, DIA & PRM analysis in a single workflow. Wanna know how CHIMERYS works? 👉 nature.com/articles/s41592-0… #TeamMassSpec #NatureMethods #ASMS2025 🧪🔬 1/7

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...

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Replying to @msaid_de @naturemethods
Following the preprint of this work, I let Martin Frejno know that DIA-NN output was processed incorrectly, resulting in nonsense data and plots. Mistakes happen, but puzzling to see these weird plots still in the final version (see below). Make your conclusions :)

Apr 22, 2025 · 3:02 PM UTC

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Replying to @msaid_de @naturemethods
How do authors explain this quantification problem with Chimerys?
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"CHIMERYS v.4.0.21 finished the analysis of the dataset 4.9 times faster than DIA-NN" "Runtimes include spectral library generation" Why include something that is done only once? It's like including the time to install the software.
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Replying to @DemichevLab @msaid_de @naturemethods
We did not change the plots, because Q.Value is the run-specific precursor q-value according to github.com/vdemichev/DiaNN/b…. This x-axis is the same for all softwares we compared. You can find your suggested version of Extended Data Fig. 6B below. How do you interpret it?
Definition of Q.Value according to the DIA-NN README.md

ALT Definition of Q.Value according to the DIA-NN README.md

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And there's a clear instruction that Lib.Q.Value filter is mandatory with MBR (link to 1.8.1 user guide github.com/vdemichev/DiaNN/t…, see screenshot below), and I explained it in detail in Twitter DMs. All this time I've been convinced that you would of course fix this.
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