Why generate an in silico-predicted library in the first place?

[FDelalande]

Hello,

In the version 1.9.2, i have this error message :

"WARNING: it is strongly recommended to first generate an in silico-predicted library in a separate pipeline step and then use it to process the raw data, now without activating FASTA digest"

Why do this in 2 steps when with older versions there was only one step: DIA-NN did the spectral library before processing the analyses?

Merci

François

[vdemichev]

Hi Francois,

Several reasons:

1. Library can be reused - saves time.
2. Library as a result of prediction will depend on the CPU instruction set - so generating just once aids reproducibility.
3. A bit less RAM usage.
4. And this is the main reason really: we do not want to support two modes for the same task, i.e. 'on-the-fly generation and raw data analysis' is not being validated properly.

Best,
Vadim