peptides quant from DIA NN report.

[QinCedars]

Hello,
I would like to extract the peptide quant from DIANN report ( the largest TSV file). I only see columns with PG.Quantity /Genes.Quantity, and Precursor.Quantity. I do have following questions:

1. Does Precursor Quantity mean MS1 quant?
2. Where Can i find exported peptide Quantity?
3. How does the Peptide quantity calculated?
4. Where could I find Ion quant for each peptide?
5. Is proteolytic sequence (Proteotypic column in the report) a unique peptide to entire human proteome? 
   Thanks for this useful tool.
   Qin

[vdemichev]

Hi Qin,

Please see the DIA-NN manual for more detail on the quantities produced. Precursor.Quantity and Precursor.Normalised are MS2 based. See examples here https://github.com/vdemichev/diann-rpackage on how to calculate peptide quantities. Individual fragment quantities are indeed saved in the final report, and listed separated by ';' - both before and after interference removal. Proteotypic = specific to the protein isoform/protein/gene (depending on 'Protein inference' setting).