disable spectra addition to library ?

[JM-Bader]

After the first pass search, DIANN adds spectra (presumably better scoring ones) to the library - it goes through every file to do this.

With deep libraries, this benefit is small. However, it is a very time-consuming step, especially in large studies.

Can one disable that process to save time?

[vdemichev]

Can set Library generation to IDs, RTs and IM profiling.

[JM-Bader]

Thanks for the swift replies.
I will try setting it to IDs, RT, and IM profiling.

If that change of settings does remove the DIANN search steps of adding the spectra of single raw files to the library, then this should (conceptionally) affect both PTM and regular peptides. Isn't it?

Or maybe the difference between i) smart profiling and ii) IDs, RT, and IM profiling is more/different than just removing the spectra addition to library steps ?

[vdemichev]

It affects everything, it's just Smart proifiling is only beneficial in PTM scenarios when in silico spectra prediction did not work well enough.

[JM-Bader]

When using IDs, RT & IM profiling, the library size appears to differ for first and second pass with less detectable in the second pass search.

First pass: 28200 library precursors

Second pass: 13354 library precursors

Q1: Why is that ? I would expect that the library has (at least) the same size of precursors. Anyway, halving the library seems quite extreme.

[vdemichev]

MBR :) Please see the docs on it

[JM-Bader]

ah ok!
I first noticed this with the IDs, RT, & IM profiling setting - so I thought it is specific to that setting.
In fact, it equally occurs with smart profiling.