Figure 4From: ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometryTransition list. ATAQS sends the protein list to the Peptide Atlas Best SRM Transition website and generates the best peptide set based on an empirical score that uses a user-defined penalty weight. For example, the user can increase the penalty value to 2 to avoid a methionine in the peptide sequence.Back to article page