Hi,
I have a proteomics experiment with 6 samples (3 controls and 3 treatments), each measured in DIA mode with three CVs per sample. I'm currently running MaxQuant on all files together, but it’s taking a very long time.
Would it be possible to run MaxQuant separately on each sample (i.e., six runs in total), then combine the resulting intensity tables and run directLFQ afterward? This approach would speed up my analysis by more than sixfold.
Thanks in advance for your advice!
Hi,
I have a proteomics experiment with 6 samples (3 controls and 3 treatments), each measured in DIA mode with three CVs per sample. I'm currently running MaxQuant on all files together, but it’s taking a very long time.
Would it be possible to run MaxQuant separately on each sample (i.e., six runs in total), then combine the resulting intensity tables and run directLFQ afterward? This approach would speed up my analysis by more than sixfold.
Thanks in advance for your advice!