Maybe a way to increase protein quantification accuracy

[Chen-proteomics]

hello, I generate a heavy labeled peptide library, and according to this library. Based on this library, I am able to categorize the peptides identified by DIA-NN into two groups: group one consists of peptides further validated by the heavy labeled peptide library, while group two includes peptides not identified in the heavy labeled peptide library. I found that the peptides from group one demonstrate better quantitative accuracy compared to the other peptides. Is it possible in DIA-NN to incorporate a function that increases the weight of specific peptides when calculating protein quantification values from peptide-level data? This could potentially improve the accuracy of protein quantification. Thank you!

[vdemichev]

Hi,

Agree, this would indeed make sense. In general, the way we do it in QuantUMS essentially leverages the same concept, although of course leveraging extra information, that is the quantities of heavy labelled counterparts, should be further beneficial (QuantUMS does use it, but probably not to the its fullest potential).

Best,
Vadim

[Chen-proteomics]

Hi Vadim，
Thank you very much for your reply : )
Is it possible or is there any way to add this extra information into DIA-NN algorithm？for example, the user define the double confirmed peptides ,and these peptides will gain their weight when calculating the protein quantitation information.

Best,
Chen