A Few Examples

Large Projects

TFE is designed for visual inspection of individual peaks. However, in studies with more than 500 samples, reviewing every peak can become time-consuming. Exact workflows will vary by study, but the following suggestions can help make review more efficient.

  • First, check the mass calibration and make sure your peaks are not close to the edge of the extraction window. For example, if your XIC window is set to 10 ppm, but most samples are appearing near 9.4–9.5 ppm from the expected m/z, you may need to widen the window or update the target m/z.

  • If there is retention time drift, inspect the first and last samples to estimate the full retention time range. Update the expected RT to a value near the middle of the observed range, then set the peak search range wide enough to cover the extremes.

  • Try sorting samples by injection order, which is usually the default order, then plot retention times in the Sample Profile Chart. Outliers should be easy to identify. These may represent missed peaks or incorrect integrations.

  • If the integrated peak is noise, click the x on the chart to scroll to that sample, then clear the annotation.

  • If a metabolite has a retention time that does not match the overall trend, it may be a single-sample issue, or TFE may be picking a different feature that happens to appear near the expected location. To investigate this, sort samples by retention time and scroll through them with the Sample Profile Chart open. Check whether other annotations around the same retention time show similar behavior.

  • We recommend removing peaks with fewer than 5 scans, since this is usually near the practical limit of detection and often represents noise.

We are working on additional guidelines for more streamlined review workflows.