Bias, randomization, and ovarian proteomic data: A reply to "Producers and Consumers"

Proteomic patterns derived from mass spectrometry have recently been put forth as potential biomarkers for the early diagnosis of cancer. This approach has generated much excitement, particularly as initial results reported on SELDI profiling of serum suggested that near perfect sensitivity and specificity could be achieved in diagnosing ovarian cancer. However, more recent reports have suggested that much of the observed structure could be due to the presence of experimental bias. A rebuttal to the findings of bias, subtitled "Producers and Consumers", lists several objections. In this paper, we attempt to address these objections. While we continue to find evidence of experimental bias, we emphasize that the problems found are associated with experimental design and processing, and can be avoided in future studies.