sample fractions

[johnpleid]

Hi to everyone
I am very new with DIA NN
If I have a sample splitted in two fractions (E.G. phospho enriched LC MSMS and unbound fraction LC MSMS) ho can I set the research to merge the identifications of the two LC MSMS runs?
Thnak u
Gio

[vdemichev]

Hi Gio,

It's currently not possible to merge these automatically in DIA-NN. But one can alsways do this in R or Python using whatever custom algorithm is best suitable for the given experiment. For this, it's probably better to use non-normalised data.

Best,
Vadim

[johnpleid]

thank you

[st-pf]

Dear Vadim,

is this feature currently planned for any upcoming version?
Would also be super interested in this directly embedded in DIA-NN.

Best wishes
Stefan

[vdemichev]

Hi Stefan,

No, not planned, as the best way different fractions will need to be merged will depend on the experiment design. E.g. is it best to sum intensities in different fractions or take the maximum? At precursor or protein level? What filtering to apply?

Best,
Vadim