Abstract

High-throughput microarray analyses require digitized images in order to convert the signal intensity to numerical values. To acquire the images, laser scanners are usually used for fluorescent signal detection. However, such microarray scanners have a limited number of excitation wavelengths, take minutes to scan a slide, and are expensive. In standard transcriptional array configurations, most study designs use relatively few samples against many probes, so only a small number of scans are necessary to complete the digital image acquisition for an experimental set. However, other microarray-based procedures may be more impacted by the limitations of dedicated microarray scanners. For instance, scanning is a major rate-limiting step when using high-density reverse-phase protein lysate microarrays (RPA) (Reference 1 and Figure 1A), which we have previously described as a method to perform proteomic profiling of many protein species across many samples. Because RPA signal detection employs a specific primary antibody followed by the catalyzed signal amplification colorimetric detection system (CSA; DakoCytomation, Carpinteria, CA, USA), whose final product is the dark-colored stain diaminobenzodine (DAB), signals can be obtained using the reflective mode of an ordinary optical flatbed scanner. Hence, we have been using optical flatbed scanners because of their fast scanning, relatively compact file size, and wide availability. However, there are several issues to be considered when using these scanners for quantitative applications.



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