Question about Fragment Intensities

[SahilCh95]

Hello,

Thank you for developing DIA-NN.

I am new to DIA-NN and mass spec in general. I am currently trying to use DIA-NN to extract fragment level data and have successfully managed to run it to analyze my samples. I am able to extract information relating to protein names, peptide, fragment information (Frag.Info) as well as the fragment intensities (Frag.Raw.Quant) from the report.tsv file. I am currently using R to process this information but I have noticed that sometimes the same fragment, derived from the same peptide (and protein), has maybe 2 intensities assigned to it. I am a little confused as to why that would happen and if that's normal or if there's something wrong with my code. Any help would be appreciated.

-Sahil