ASAPRatio is designed for isotopic labeling datasets such as biological incorporation SILAC or chemical approaches such as dimethylation or older ICAT and similar approaches to labeling samples. ASAPRatio also reads as input a protXML file as well as the corresponding pepXML and mzML files, deriving abundance measurements based on the MS1 profiles of the precursors. In addition to the automatic first pass quantitation, ASAPRatio has a manual-inspection mode whereby outlier signals can be inspected to see if the measurements seem accurate or if interfering ions have contaminated the measurements, allowing the user to adjust quantitation or discard individual measurements. Corrected abundance measures are automatically rolled back up to the protein level.