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Determining the Signal-to-Noise Ratio and Optimal Photomultiplier gain setting in the GenePix 4000B

over the full range of PMT voltages for a single spot in the middle of a dilution series (A, below saturation at 1000 V), and near the detection limit (B, defined as SNR = 3).


2. Effect of PMT Gain Over Full Range of Fluorescent Concentrations.
A dilution series of dyes Cy3 (Figure 2A) and Cy5 (Figure 2B), spanning six orders of magnitude, were scanned over the entire range of PMT voltages. At any dye concentration, the SNR improves from 200 V to about 500 V. Above 500 V, the highest spots in this dilution series begin to saturate, so the linear range is reduced at the top end. There is no difference in detection limit for either dye at a PMT gain between 500 V and 900 V.

Figure 2: SNR over a full range of PMT voltages for both the Cy3 (A) and Cy5 (B) was measured for a dilution series spanning six orders of magnitude.


Conclusion
For a wide range of Cy3 and Cy5 conecntrations, the optimum PMT gain on the GenePix 4000 Array Scanners is anywhere in the range from 500 V to 900 V, as long as the brightest signals are below saturation.

Further reading
Basarsky, T., Verdnik, D. Zhai, J.Y. and Wellis, D. Overview of a Microarray Scanner: Design Essentials for an Integrated Acquisition and Analysis Platform. pp 265-284. In: Microarray Biochip Technology. M. Schena (Ed.), BioTechniques Books, Natick, MA. (2000)


* Most laser-base arrray scanners use PMTs for detection. PMTs convert photons striking one end of the detector into electrons, and then amplify the electrons as they pass through to the other e
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