AS-MS Peak Area Thresholds
Setting the right peak area threshold can slash AS‑MS false positives while keeping true hits
AS-MS Peak Area Thresholds
Setting the right peak area threshold can slash AS‑MS false positives while keeping true hits
Optimizing Peak Area Thresholds in AS-MS Background Filtering
How much difference should there be in the peak area between the original hit and the potential cross-hit? It turns out that this is a key parameter and, if it's set improperly, you can see a significant increase in your false positives.
Experiment
Using a 250,000 compound AS-MS library spread across 96 wells, Virscidian scientists worked to determine what defined “similar” with respect to peak areas when searching for possible cross-hits.
Key Finding
After analysis of the 82,314 background ions, scientists discovered that a threshold of 55% difference in peak areas between background ions and the potential hits captured approximately 97% of all the potential cross-hits.
Recommended Practice
Using Virscidian’s automated cross-hit filter with an area difference threshold of around 55% maximizes background cross-hit filtering while preserving true hits. Tighter thresholds increase false positives; looser ones offer diminishing returns.
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