From Pawel:
Currently, upon right mouse button click on a MSMS spectrum, one can tell Skyline to highlight a, b, c, x, y, z ions as well as a precursor ion. I would appreciate if two more ion types could be highlighted and dehighlighted in the same way, namely: neutral loss peaks and immonium ions.

Currently there is no support for immonium ions at all (and this has been reported in a separate post) and regarding neutral loss peaks, once the information about neutral loss has been added to the modification, neutral loss peaks are always highlighted in a MSMS spectrum and to dehighlight them one needs to remove them from the modification. It would be great if highlighting/dehighlithing of neutral loss peaks and immonium ions could be done simply upon right mouse click.

For the moment, lets just add the menu item that allows neutral loss ions to be turned on and off. We can come back to the immonium ions later.

Also, could now show custom ions.

Just to get the two bugs assigned to the same place before going to Tobi, and because I think your recent focus on small molecule libraries make you the more appropriate person to lead this work, I am assigning this to you, Brian.

Giving this to Rita also, so that a single person owns our spectrum annotation feature improvements.

Neutral loss annotation have been added. I don't know if we still plan to support immonium ions.