High-resolution serum proteomic patterns for ovarian cancer detection

We read with interest the review article by Conrads et al. (2004) on the use of high-resolution proteomic profiling of serum for ovarian cancer detection, noting in particular the authors’ claims of 100% sensitivity and specificity. Unfortunately, an aspect of the paper causes us great concern, as it suggests the possible presence of substantial experimental bias. The source of our concern is contained in Figs 6A and 7 of Conrads et al. (2004). In Fig 6A, the record number (number of non-zero entries) in each Qstar spectrum is plotted against sample number, with different symbols indicating the 3 days on which the samples were run: day 1 on the left, day 2 in the center, and day 3 on the right. As the authors note, this figure shows clearly that something was going wrong with the process near the end of the run. Figure 7 shows the record numbers of the files remaining after the application of a quality control filter against sample number, with controls on the left and cancers on the right. As can be seen in Fig 1 of this letter, when these two plots are superimposed, they coincide perfectly. This