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vdemichev / DiaNN

DIA-NN - a universal automated software suite for DIA proteomics data analysis.
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PG.MaxLFQ & SILAC #1123

Open Giu-F opened 3 months ago

Giu-F commented 3 months ago

Hi Vadim, I read that PG.MaxLFQ in the main report is channel specific. Is it calculated using only precursors passing the q value threshold recommended for SILAC? Q.Value <= 0.01 Lib.Q.Value <= 0.01 PG.Q.Value <= 0.05 Lib.PG.Q.Value <= 0.01 Channel.Q.Value <= 0.01 Translated.Q.Value <= 0.01

Thanks, Giulia

vdemichev commented 3 months ago

Hi Giulia,

Yes, it's calculated using Channel.Q.Value <= 0.01 and Q.Value <= 0.01 filters.

Best, Vadim

Giu-F commented 3 months ago

Ok, thanks. Shall I still apply all the filters mentioned above to the main report before generating a protein group matrix?

vdemichev commented 3 months ago

For protein group matrix (provided you use QuantUMS and PG.MaxLFQ generated by DIA-NN) you don't need these: Channel.Q.Value <= 0.01 Translated.Q.Value <= 0.01

Other filters you listed - yes.

Giu-F commented 3 months ago

Ok great. If working on the precursor level (e.g. when doing phosphoproteomics), do you still recommend to filter for both Channel.Q.Value <= 0.01 and Translated.Q.Value <= 0.01? Or Channel.Q.Value <= 0.01 is enough?

vdemichev commented 3 months ago

Only Channel.Q.Value <= 0.01.

Also, in any case, when using QuantUMS, please add either Quantity.Quality > 0 (precursor-level) or PG.MaxLFQ.Quality > 0 (protein level).