Fragment ion type matches in PD2.2 and 2.3

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Erik de Graaf

May 22, 2019, 11:46:00 AM5/22/19
to MS Amanda
Hi Victoria,

I used MS Amanda in PD 2.2 and 2.3 and I noticed that whenever I use neutral loss ions in the 'ion settings' box it automatically also looks at z ions. At least when looking at psm spectra the ion table and spectra shows z+1,... ions as well. This does not happen when only (a,)b,y ions are selected. I definitely want NL ion matching as well. 

Is this a bug?


Viktoria Dorfer

May 23, 2019, 9:42:05 AM5/23/19
to MS Amanda
Hi Erik,

thanks for reporting that!
I had a look at the code and it is definitely a bug but just a bug in what is reported to PD. So MS Amanda does not really score z ions when NLs are considered, it only tells PD that it did ;)
So no worries, the scoring is correct, just the visualization in PD is wrong as we report something wrong. We will fix that asap, sorry for the inconvenience!

Best regards,
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