The "Invalid transition list format. Failure parsing numeric value" error is caused by comma character (usually in the Protein name). This is because Skyline passes the transition list to a separate executable that builds the method. It passes this information as a comma separated value (CSV) text file. You can see what this looks like if you export "Transition List ..." rather than method in Skyline. The extra comma in the protein name was causing an extra column to be included, which the method building executable didn't know how to use. To avoid this problem use an alternative character.