In general we consider NPX from the two platforms (qPCR and NGS) to be on different scales, so any direct comparison between the two should be done with care. We have seen in our internal qPCR versus NGS comparisons that the correlation is on average good, above 0.75, but some proteins have a low correlation. Proteins with lower correlations tended to have limited spread in at least one platform and/or were typically close to the limit of detection.
We would advise to plan the analysis in such a way that you do not rely on the direct comparison of NPX values between the two platforms. It should be sufficient in most cases to analyze data from each platform separately and then compare the results (p-values and directions). There must be compelling reasons for combining Target 96 data with Explore data, since the quality for some proteins is reduced, and thus the usefulness of direct comparisons will be protein dependent. If data must be combined, at least 24 overlapping bridging samples should be included and data combined using the same method as for combining Target 96 runs or Explore runs (median adjustment).
For any bridging normalization to be successful, the bridging samples need to represent the study samples well and need to be within the dynamic range of most assays.