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Topic: LC-MS pre-treatment and filtering (Read 2222 times) previous topic - next topic

LC-MS pre-treatment and filtering

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!