I was playing around with some small molecules, and a few are analyzed in negative polarity. They were imported to Skyline with -1 for the precursor and product charge states. When exporting the Isolation lists for Thermo Fusion, this polarity is not handled correctly. The charge state z field is set to -1 for these compounds, which the Thermo method editor highlights as an error. Instead, the z field should be written as a 1, and there should be a column with the Polarity header, with the string Positive for the positive compounds, and Negative for the ones with negative z. This is handled correctly for exporting transitions lists to the Thermo Altis, however.

I was trying to optimize some collision energies by hand, and running into the fact that one cannot optimize parameters for Isolation lists. This ability would be very useful for small molecule work.

Thanks
Philip