Quantity.Quality

[NicoDrou]

Dear Vadim,

I would have some questions about the Quantity.Quality. In a previous discussion (https://github.com/vdemichev/DiaNN/discussions/764), you explained this parameter can filter the precursors and keep the high-quality ones. You even suggested a threshold of 0.8 as a basic threshold. However, in a new post, you mention it only makes sense when using QuantUMS (https://github.com/vdemichev/DiaNN/issues/1091).

Therefore, could you confirm we can or shouldn't use the Quantity.Quality to filter our precursors before using the maxLFQ algorithm? What about using a RSD filtering based on QC samples? I have the example of peptides with a RSD of 20% across 60 technical replicates spread over 10 batches but with a Quantity.Quality of 0! What would you trust the most to keep the best precursors for quantification? By the way, are you planning to add a QuantUTM function to your DIA-NN R-package? :D )

Also, in the README you give this definition of the Quantity.Quality: Quantity.Quality when using QuantUMS is equal to 1.0 / (1.0 + SD), where SD is the standard deviation of the LC-MS-derived error in relative precursor quantification But, shouldn't the Quantity.Quality of a precursor always be the same through the different analyses? Because in my case, I have close, but different values at each analysis.

Many thanks in advance for your help.

Best regards, Nicolas