A single ".txt" file containing the peptides and their intensities
(in each replicate), detected by MaxQuant analysis over the Flow-through fraction.
After running MaxQuant, this file can be found in the following path:
$maxquant_output_folder/combined/txt/peptides.txt
Notice that the different replications should be set as different experiments (a, b, c, etc...)
when running MaxQuant (see example configuration file
here).
Please use neither spaces nor commas in the different file names as
it might cause to an unexpected behavior.