Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI or SELDI-TOF MS) with protein arrays has facilitated the discovery of disease-specific protein profiles in serum. As array technologies in bioinformatics and proteomics multiply the quantity of data being generated, more automated hardware and computational methods will become necessary in order to keep up. Robot automated sample preparation and analysis pipeline for proteomics (Raspap) in SELDI provides a solution from the lab bench to the desktop. In this approach, the entire processing of protein arrays is delegated to a robotics system and the bioinformatics automated pipeline (BAP) performs data mining after SELDI analysis. A key part of BAP is the creation of a journal-styled report in HTML (with text, embedded figures, and references) which can be automatically emailed back to the engineers/scientists for review. An object-oriented tree-based structure allows for the derivation of conclusions about the data and comparison of multiple analyses within the generated report. Testing yielded improvement in the resulting assay coefficients of variation (CV) from 45.1% (when done manually) to 27.8% (P<0.001). A large biological dataset was also examined with the Raspap approach and consequent results are discussed.