Time and time again, it's always the same picture. DIA-NN controls FDR correctly as data reliability has been the main goal at DIA-NN's conception back in 2017 and a priority since then. Data from a very nice paper introducing the Thin-diaPASEF concept: doi.org/10.1093/dnares/dsaf0….

Last edited Jul 25, 2025 · 11:23 AM UTC

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Replying to @DemichevLab
That's an interesting statement when it was recently shown in multiple publications (e.g. nature.com/articles/s41592-0…) that DIA-NN v1.8.1 (superseded by v1.9 shortly after ASMS 2024) does not consistently control FDR. Great to see that more recent versions seem to have improved here.

Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment

Nature Methods - A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass...

nature.com
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Indeed, Bo Wen and colleagues found a particular dataset on which 1.8.1 was producing inflated FDR. We investigated this and changed the algorithms. But even then, DIA-NN was still the more accurate one among DIA softwares. Also some credit goes to you for making such a big fuss of it :)
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Replying to @DemichevLab
Nice !!
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