Skyline is a comprehensive package for building and optimizing multiple reaction monitoring (MRM) assays. Proteins and peptides can be loaded into Skyline from previous results or pasted from Microsoft Excel or from library data. Then, using predictive algorithms, the best charge state and fragment ions for each peptide are chosen for the acquisition method. The user has complete control over peptide settings and transition settings and can specify the number of transitions per method, a standard or Scheduled MRM™ Assay method, set up parameter optimization, or browse to a template method that can have all chromatographic settings included.