andyzim111

Thanks for your reply. I noticed that multiple phosphorylated peptides has only one PTM localization confidence in DIA-NN reports, and then which one phosphosite does the confidence correspond to?

I got it. The localisation score shows the likeliness that the whole phosphopeptide bearing modifications is present or not, this kind of like "peptidoform".

Thanks for the quick response. How can I get the sample-specific peptide or protein intensities if all samples were analyzed together in DIA-NN? Just sum the intensities from all fractions...

Thanks for the quick response. How can I get the sample-specific peptide or protein intensities if all samples were analyzed together in DIA-NN? Just sum the intensities from all fractions...

> Visualisation of peptide positions is now possible with https://github.com/MannLabs/alphamap Thanks a lot.