SILAC quantification using multiple labels

[brucewayne949]

Hi Vadim and everyone

I was trying to quantify a DIA dataset which contains +4 and +8 heavy labelled lysines only (and not arginines). Based off previous SILAC discussions, I thought this is how the the 'additional options' should look like, but I'm not sure.

--reanalyse
--smart-profiling
--fixed-mod SILAC,0,K,label
--lib-fixed-mod SILAC
--channels SILAC,L,K,4.00078; SILAC,H,K,8.05021
--peak-translation
--original-mod

Is it possible to quantify data containing more than one heavy label using DIA-NN?

[vdemichev]

Hi,

Sounds correct, should work, but also please see the description of multiplexed data analysis here: https://github.com/vdemichev/DiaNN?tab=readme-ov-file#multiplexing-using-plexdia

Best,
Vadim

[vdemichev]

Mass on H lysine seems incorrect though

[brucewayne949]

Thanks Vadim!