Frequently Asked Questions


Q: How do I optimize IntelliXtract input parameters?

A: Refer to this Technical Note for step-by-step instructions

Q: How can I add a label to chromatographic peaks?

Q: Enter IntelliXtract mode, and click Options. Select the Ion Presence tab. Enter the mass or chemical formulae for the neutral molecule, and the label. In the Mode column, choose Ref (Reference) mode if you only wish to label that compound. Alternately, choose Parent mode if you would like to label the compound, plus any common Modifications or biotransformations (e.g., hydroxylation).

Click Modifications to see the list of built-in metabolic transformations. You can also add your own to the list

Q: No peaks are present in the Table of Mass Chromatograms.


  • Check the column headers to make sure you have turned off all Advanced Data Filters.
  • You may need to optimize your peak picking options, and reprocess the data.