LC-MS pre-treatment and filtering February 15, 2022, 10:13:21 AM Hi everyone, I have no experience with LC-MS data acquisition or analysis, but I should work on untargeted metabolomic datasets acquired by someone else previously. Every plasma sample was analysed in triplicate. Therefore, when I open the entire chromatogram to do a primary visual inspection, the replicates of the same samples do not perfectly coincide. To say more, some peaks of the same sample seem to have a completely different profile in consecutive runs. In this case, should I consider one of the runs as an outlier and eliminate it? Generally speaking, how should I pretreat the raw LC-MS data? Another doubt is about the blanks. I noticed that all the samples were acquired without blanks; if I do not have blanks, how can I filter and normalise after my spectra?I hope to be clear enough.Thanks in advance! Quote Selected