MaxQuant 2.0.3.0 is not reporting iBAQ values?

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Nils Rugen

Hi Sebastian,

do you get no iBAQs at all or is it just not working for all of your proteins?

Best,

Nils

Sebastian Hoernstein

unfortunately I don´t get iBAQ values for any protein....

Maybe database problem?

What Database do you use? Something custom?

And do you get any Peptide intensities in "peptides.txt"?

Hi,

yes it´s a custom database in fasta format. I get intensities in the peptide.txt file, also LFQ values are provided.

If anyone had the same problem, I found it. iBAQ does not work when semispecific protease specificity is chosen. Somewhat logic ....