Are doubly charged fragment ions considered?

[glormph]

Hi Yafeng! :)

We recently had an ion that was MKD......, with TMT where the b ion series was doubly charged, due to the K in the second position. I guess that is not very common, especially since it also represents a missed cleavage.

I'm not super sure about this, but SpectrumAI failed this peptide and maybe does not consider the 2+ ions. When checking by hand, we saw that there was a complete b ion series, while a y flanking ion was missing. It's not super important to us right now, but may be good to know and I'm posting it also for my own reference :)

[yafeng]

@glormph
Hi, Jorrit! I have read your message, can you illustrate in details or paste out SpectrumAI predicted b, y ions list? I remember there is an option to predict 2+ ions as well. Mabye you can try setting product_ion_charge =2 ?

predicted_peaks = predict_MS2_spectrum(Peptide = peptide, product_ion_charge = 1)

Yafeng