Figure 1

Primary Processing Tasks within the APEX Quantitative Proteomics Tool. The flowchart illustrates the three major processing tasks within the APEX tool. Processes are depicted in rounded rectangles while data inputs are shown as rectangles where bold rectangles indicate data that is generated by the APEX tool. The first two processes have the objective to produce O _i values while the last process, enclosed in the larger rounded rectangle, uses these O _i values to quantify proteins based on the supplied MS results imported in protXML format. Note that O _i values only need to be generated once to support quantitation of proteins from the particular proteome under study. Once created, these O _i values can be used repeatedly for the same proteome analyzed on the same MS instrument.