Thank you for your reply.
Actually I have 6 mass spectrometry runs recorded in Agilent QTof . Out of the 6 runs , three runs corresponds to diabetic mouse metabolites and other three runs belong non-diabetic mouse metabolites. I want to see total how many metabolites are characterised and present in total 6 mass spectrometry runs, then I would like to quantify the metabolites. Please let me know how to run the data using skyline. How to convert Agilent QTof MS/MS files to skyline files ?
Thank you for help.