Intact protein LC/MS analysis can provide a wealth of information about a biopharmaceutical, and the process by which it was created. Processing of data sets typically follows a generic workflow, making processing/annotation of large data sets a repetitive and often tedious process. Automated processing of intact protein LC/MS data has been accomplished (e.g. automated MaxEnt1 data processing under the open access program OpenLynx), but has not encompassed annotation of deconvoluted protein masses to their likely structures, nor facilitated direct comparisons between individual results. This poster describes ongoing efforts to integrate all such capabilities in to a single application geared towards automated analysis of protein infusion and LC/TOF-MS protein data. We will highlight the rationale used to process intact protein LC/MS data, assign masses to proteins and their variants, and illustrate various approaches for inter-sample comparisons. This poster was presented at Mass Spec 2007: Fourth Symposium on the Practical Applications of Mass Spectrometry in the Biotechnology and Pharmaceutical Industries.