Abstract: Methods, systems and GUIs for defining a sequence of analyzes for an analytical instrument using a workflow are described. A method includes receiving user inputs including workflow parameters for defining the sequence, and automatically defining the sequence for the analytical instrument based on the workflow parameters, including creating rules for the sequence. The rules are persistent for subsequent use of the sequence. The rules are defined by the user, e.g., an administrator, who creates or edits the workflow. The administrator can leave some choices available to operators who run the workflow, or can lock selections down.