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I'd like to do a targeted screening analysis for trace contaminates. However, due to the nature of the sample preparations, the retention times I'm getting drift a lot from run to run and XCMS isn't properly identifying my standards and thus affecting my ability to evaluate my samples.

Is there some trick to getting XCMS to identify the proper retention time that I'm missing?

Is there some other software I should be using? (We have several different instruments from different vendors so it's better if it's not tied to the particular MS)

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  • $\begingroup$ I'm not an expert of mass spectrometry, but perhaps showing the figures or some data might provide an expert with some clues to help you. $\endgroup$
    – llrs
    Commented May 11, 2018 at 7:37
  • $\begingroup$ As Llopis said, some more details should help to attract an answer. Particularly, which version of XCMS and showing XIC's from some of your standards to show the run-run variation. $\endgroup$
    – Michael_A
    Commented May 13, 2018 at 10:00

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