Is there an actual dependency on Fragpipe-DIA

[sooheon]

The quickstart mentions one should use output of Fragpipe-DIA as input to the analyst

For protein: Upload protein group (PG) matrix ( diann-output.pg_matrix.tsv ) generated by DIA-NN in FragPipe
For peptide: Upload precursor group matrix ( diann-output.pr_matrix.tsv ) generated by DIA-NN in FragPipe

But I can also use DIA data searched and quantified by DIA-NN directly, correct? I assume there is no additional column that FragpipeDIA adds that this tool depends on.

[hsiaoyi0504]

I think there is still some difference like DIA-NN result might contain multiple proteins reported, see Nesvilab/FragPipeAnalystR#14.