How to Add Additional Amino Acids into Molecule Profiler Custom Elements List

For research use only. Not for use in diagnostic procedures.

Answer

The custom amino acids that are needed to define a peptide with unnatural amino acids are entered via the “Custom Elements” found under the “Edit” menu. Shown below is an example. Please ensure to enter the residue formula (i.e HN-HCR-CO) not the full amino acid formula (i.e H2N-HCR-COOH).
Entries have to added this one by one via “New” button in the dialog.


The other option would be to edit the Custom AA.xml that can be found at C:\ProgramData\SCIEX\ElementalCalculator.
Here is what the customAAData.xml looks like upon opening.  Please note that the entry {2A} was added before via the above described workflow.

Edit the XML file as shown below and save it. Close and open Sciex OS so that edits to the .xml are initialized. Once you navigate to Custom Elements the new entry is available.


The new entries are now listed in the Custom Elements AA List