What is needed to use AlphaDIA's QuantBuilder for quantification?

[rodvrees]

• Per run: a folder containing a file called “frag.parquet” (it’s hardcoded in alphadia)
• This frag.parquet should contain the columns “precursor_idx”, “number”, “type”, “charge”, “intensity” and “correlation”
• A psm_df which contains the column “precursor_idx”, which is used to link to fragment data

Example files:
mumdia_quant_necessities.zip

The "type" column, in AlphaDIA, contains 98 for b ions and 121 for y ions, needs to be an int for the hash creation, as far as I understand, as well as "number" and "charge"

[rodvrees]

df_fragment, before passing to mumdia.main, already contains the following columns:
psm_id, fragment_type, ordinals, fragment_charge, fragment_intensity. So it's only missing a correlation column.