u/Born-Word4192

Hello there, we have performed a pulsed SILAC experiment to measure nascent translation. And to get a greater coverage we did extensive peptide fractionation and dia a DIA based measurement on Orbital Astral. However now we are stuck at the data analysis/ search part since DIANN is not meant for fractionated datasets.

Does anybody have similar experiences and can suggest how to move forward with searching this dataset (which was quite easy in Max quant by entering peptide fractions) . without DIA and peptide fractionation we do not get a lot of H/M precursors at early time points which is where we believe our interest lies.

Any help is highly appreciated.