When building a MRM method in Skyline for use in Analyst® 1.6.1 software, the following error may appear: "Invalid transition list format. Failure parsing numeric value".
Skyline passes the transition list to a separate executable that then builds the method. The information is passed on as a comma separated value (CSV) text file. The extra comma in the protein name was causing an extra column to be included, which the method-building executable could not read.
Remove any commas from protein names; backslashes, underscores or pipes / _ | can all still be used.