I was wondering if there is a faster way to get all identifications back, without applying FDR?
I am using now the following line of code for that:
It returns about 10000 psms with FDR = 1 (so, I thought all ms/ms spectra)
However, if I look to my mgf file, there are about 15000 spectra over there. How does it come that with FDR = 1 this number is not the same? And, how could this be improved?